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Journal articles on the topic 'SNP development'

Author: Grafiati

Published: 4 June 2021

Last updated: 12 February 2022

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1

Dixon, L. A., P. Koumi, and Peter Gill. "Development of an autosomal SNP multiplex containing 20 SNP loci plus Amelogenin." International Congress Series 1288 (April 2006): 31–33. http://dx.doi.org/10.1016/j.ics.2005.08.041.

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2

Kim, Jae-Jung, Bok-Ghee Han, Hae-In Lee, Han-Wook Yoo, and Jong-Keuk Lee. "Development of SNP-based human identification system." International Journal of Legal Medicine 124, no. 2 (November 18, 2009): 125–31. http://dx.doi.org/10.1007/s00414-009-0389-9.

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3

Gangopadhyay, Debnirmalya, Ashmita Ghosh, and Mrinal Ray. "Seribiodiversity and their Role in Sustainable Development in India." INTERNATIONAL JOURNAL OF PLANT AND ENVIRONMENT 5, no. 04 (October 31, 2019): 243–46. http://dx.doi.org/10.18811/ijpen.v5i04.3.

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Nitric oxide (NO) is an important bioactive signaling molecule in plants which modulates a variety of physiological processes and responses to abiotic and biotic stresses. In this study, the effects of exogenous NO supplied as sodium nitroprusside (SNP) in wheat seedlings under ironinduced oxidative damage was investigated. An appropriate concentration of NO was determined by conducting a preliminary experiment. In solution culture, wheat seeds were grown in the control (100 μM Fe), and toxic Fe (400 μM Fe) levels and the toxic Fe supply was treated with various levels of (50, 100, 200 and 500 μM) sodium nitroprusside (SNP). The results indicated that 400 μM Fe significantly decreased percentage germination, tolerance index, root lengths as well as fresh and dry weight compared to control. Exogenous SNP attenuated the inhibition of wheat seed germination. The promoting effect was most pronounced at 100 μM SNP. The accumulated concentration of iron and active Fe was significantly decreased by SNP treated Fe toxic seedlings. Toxicity of Fe caused oxidative stress by elevating hydrogen peroxide (H2O2), malondialdehyde (MDA) and proline contents in roots of wheat seedlings. One hundred μM SNP counteracted Fe toxicity by reducing the H2O2, MDA and proline contents of toxic Fe exposed seedlings. Meanwhile, application of SNP markedly reduced the activities of superoxide dismutases (SOD), catalases (CAT), peroxidase (POD), ascorbate peroxidases (APX), non protein thiols (NPT) and of glutathione reductase (GR) and increased ascorbate (ASc) compared with Fe toxic treatment alone, thereby indicating the modulation of the antioxidative capacity in the root under Fe stress by NO. The results indicated that the exogenous application of SNP, improved the antioxidant enzymes activity of wheat seedlings against Fe induced oxidative stress.

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4

Chagné, David, Ross N. Crowhurst, Michela Troggio, Mark W. Davey, Barbara Gilmore, Cindy Lawley, Stijn Vanderzande, et al. "Genome-Wide SNP Detection, Validation, and Development of an 8K SNP Array for Apple." PLoS ONE 7, no. 2 (February 21, 2012): e31745. http://dx.doi.org/10.1371/journal.pone.0031745.

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5

Kim, Sang-Wook, Xiaoping Li, Yun-Mi Lee, Jong-Joo Kim, Tae-Hun Kim, Bong-Hwan Choi, and Kwan-Suk Kim. "Development of SNP Markers for Domestic Pork Traceability." Journal of Animal Science and Technology 52, no. 2 (April 30, 2010): 91–96. http://dx.doi.org/10.5187/jast.2010.52.2.091.

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6

Zar, Mian Sahib, Ahmad Ali Shahid, Muhammad Saqib Shahzad, Kyoung-Jin Shin, Hwan Young Lee, Sang-Seob Lee, Muhammad Israr, Peter Wiegand, and Galina Kulstein. "Forensic SNP Genotyping with SNaPshot: Development of a Novel In-house SBE Multiplex SNP Assay,." Journal of Forensic Sciences 63, no. 6 (April 10, 2018): 1824–29. http://dx.doi.org/10.1111/1556-4029.13783.

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7

Ellonen, P., M. Levander, I. Ulmanen, and M. Lukka. "Development of SNP microarray for supplementary paternity testing." International Congress Series 1261 (April 2004): 12–14. http://dx.doi.org/10.1016/s0531-5131(03)01824-7.

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8

McCouch, Susan R., Keyan Zhao, Mark Wright, Chih-Wei Tung, Kaworu Ebana, Michael Thomson, Andy Reynolds, et al. "Development of genome-wide SNP assays for rice." Breeding Science 60, no. 5 (2010): 524–35. http://dx.doi.org/10.1270/jsbbs.60.524.

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9

Daniłowicz, Emilia, Mansoureh Akouchekian, Cord Drögemüller, Bianca Haase, Heidi Kuiper, Ottmar Distl, Tosso Leeb, and FUGATO-consortium IRAS∗. "Molecular Characterization and SNP Development for the PorcineIl6andIl10Genes." Animal Biotechnology 19, no. 3 (July 7, 2008): 159–65. http://dx.doi.org/10.1080/10495390802088621.

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10

Ferraz, J. B. S., X. L. Wu, H. Li, J. Xu, R. Ferretti, B. Simpson, J. Walker, et al. "Development and evaluation of a low-density single-nucleotide polymorphism chip specific to Bos indicus cattle." Animal Production Science 60, no. 15 (2020): 1769. http://dx.doi.org/10.1071/an19396.

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Context Genomic selection has been of increasing interest in the genetic improvement of Zebu cattle, particularly for quantitative traits that are difficult or expensive to measure, such as carcass traits and meat tenderness. The success of genomic selection depends on several factors, and at its core is the availability of single-nucleotide polymorphism (SNP) chips that are appropriately designed for Bos indicus cattle. However, the currently available commercial bovine SNP chips are mostly designed for Bos taurus cattle. There are two commercial Bos indicus SNP chips; namely, GeneSeek genomic profiler high-density Bos indicus (GGP-HDi) SNP chip and a low-density (LD) Bos indicus SNP chip (Z chip), but these two Bos indicus SNP chips were built with mixed contents of SNPs for Bos indicus and Bos taurus cattle, due to limited availability of genotype data from Bos indicus cattle. Aims To develop a new GGP indicus 35000 SNP chip specifically for Bos indicus cattle, which has a low cost, but high accuracy of imputation to Illumina BovineHD chips. Methods The design of the chip consisted of 34000 optimally selected SNPs, plus 1000 SNPs pre-reserved for those on the Y chromosome, ‘causative’ mutations for a variety of economically relevant traits, genetic health conditions and International Society for Animal Genetics globally recognised parentage markers for those breeds of cattle. Key results The present results showed that this new indicus LD SNP chip had considerably increased minor allele frequencies in indicus breeds than the previous Z-chip. It demonstrated with high imputation accuracy to HD SNP genotypes in five indicus breeds, and with considerable predictability on 14 growth and reproduction traits in Nellore cattle. Conclusions This new indicus LD chip represented a successful effort to leverage existing knowledge and genotype resources towards the public release of a cost-effective LD SNP chip specifically for Bos indicus cattle, which is expected to replace the previous GGP indicus LD chip and to supplement the existing GGP-HDi 80000 SNP chip. Implications A new SNP chip specifically designed for Bos indicus, with high power of imputation to Illumina BovineHD technology and with excellent coverage of the whole genome, is now available on the market for Bos indicus cattle, and Bos indicus and Bos taurus crosses.

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11

Kim, M. Y., K. Van, P. Lestari, J. K. Moon, and S. H. Lee. "SNP identification and SNAP marker development for a GmNARK gene controlling supernodulation in soybean." Theoretical and Applied Genetics 110, no. 6 (February 25, 2005): 1003–10. http://dx.doi.org/10.1007/s00122-004-1887-2.

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12

DeSanti, Charles L., and William R. Strohl. "Characterization of the Streptomyces sp. Strain C5 snp Locus and Development of snp-Derived Expression Vectors." Applied and Environmental Microbiology 69, no. 3 (March 2003): 1647–54. http://dx.doi.org/10.1128/aem.69.3.1647-1654.2003.

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ABSTRACT The Streptomyces sp. strain C5 snp locus is comprised of two divergently oriented genes: snpA, a metalloproteinase gene, and snpR, which encodes a LysR-like activator of snpA transcription. The transcriptional start point of snpR is immediately downstream of a strong T-N11-A inverted repeat motif likely to be the SnpR binding site, while the snpA transcriptional start site overlaps the ATG start codon, generating a leaderless snpA transcript. By using the aphII reporter gene of pIJ486 as a reporter, the plasmid-borne snpR-activated snpA promoter was ca. 60-fold more active than either the nonactivated snpA promoter or the melC1 promoter of pIJ702. The snpR-activated snpA promoter produced reporter protein levels comparable to those of the up-mutated ermE∗ promoter. The SnpR-activated snpA promoter was built into a set of transcriptional and translational fusion expression vectors which have been used for the intracellular expression of numerous daunomycin biosynthesis pathway genes from Streptomyces sp. strain C5 as well as the expression and secretion of soluble recombinant human endostatin.

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13

Peñaloza, Carolina, Diego Robledo, Agustin Barría, Trọng Quốc Trịnh, Mahirah Mahmuddin, Pamela Wiener, John A. H. Benzie, and Ross D. Houston. "Development and Validation of an Open Access SNP Array for Nile Tilapia (Oreochromis niloticus)." G3: Genes|Genomes|Genetics 10, no. 8 (June 12, 2020): 2777–85. http://dx.doi.org/10.1534/g3.120.401343.

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Tilapia are among the most important farmed fish species worldwide, and are fundamental for the food security of many developing countries. Several genetically improved Nile tilapia (Oreochromis niloticus) strains exist, such as the iconic Genetically Improved Farmed Tilapia (GIFT), and breeding programs typically follow classical pedigree-based selection. The use of genome-wide single-nucleotide polymorphism (SNP) data can enable an understanding of the genetic architecture of economically important traits and the acceleration of genetic gain via genomic selection. Due to the global importance and diversity of Nile tilapia, an open access SNP array would be beneficial for aquaculture research and production. In the current study, a ∼65K SNP array was designed based on SNPs discovered from whole-genome sequence data from a GIFT breeding nucleus population and the overlap with SNP datasets from wild fish populations and several other farmed Nile tilapia strains. The SNP array was applied to clearly distinguish between different tilapia populations across Asia and Africa, with at least ∼30,000 SNPs segregating in each of the diverse population samples tested. It is anticipated that this SNP array will be an enabling tool for population genetics and tilapia breeding research, facilitating consistency and comparison of results across studies.

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14

Utami, Dwinita W., I. Rosdianti, P. Lestari, D. Satyawan, H. Rijzaani, and I. M. Tasma. "DEVELOPMENT AND APPLICATION OF 1536-PLEX SINGLE NUCLEOTIDE POLYMORPHISM MARKER CHIP FOR GENOME WIDE SCANNING OF INDONESIAN RICE GERMPLASM." Indonesian Journal of Agricultural Science 14, no. 2 (October 16, 2013): 71. http://dx.doi.org/10.21082/ijas.v14n2.2013.71-78.

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A successful molecular breeding program requires detailed and comprehensive understanding of the diversity of rice germ-plasm and genetic base of target traits. The objective of this research was to develop the high throughput 1536-SNP chip linked to heading date and yield component traits and used it for genotyping the diverse Indonesian rice germplasm. The genotype data obtained could be used for diversity analysis and genome wide association mapping study. A 1536-SNP genome wide assay was developed using the Illumina’s GoldenGate technology. The SNP markers were selected in the rice genome regions containing heading date and yield component genes or regions where the quantitative trait loci (QTLs) of the two traits were mapped. The developed custom SNP chips were then used for genotyping 467 rice accessions showing diversity in heading dates and yield components. The assay can reliably be used for diversity analysis and mapping genes associated with heading date and yield component traits. For 1536-SNP BIO-RiceOPA-1 custom chip designed, a total of 34.832 SNPs distributed in rice genome particularly in the region of heading date and yield component genes or QTLs were identified. A total of 1536-SNP were selected and confirmed to be used for genotyping analysis. Analysis performance and quality of 1536-SNP BIO-RiceOPA1 showed that 60% (918/1536) of total SNP markers had a good differentiating power in scanning the rice accessions tested (MAF > 0.2). The 1536-SNP genome wide assay Illumina’s GoldenGate designed was useful for diversity analysis and could be used as SNP marker for large scale genotyping in rice molecular breeding involving Indica-Indica, Indica-Japonica and Indica-Tropical Japonica crosses. <br />

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15

Utami, Dwinita W., I. Rosdianti, P. Lestari, D. Satyawan, H. Rijzaani, and I. M. Tasma. "DEVELOPMENT AND APPLICATION OF 1536-PLEX SINGLE NUCLEOTIDE POLYMORPHISM MARKER CHIP FOR GENOME WIDE SCANNING OF INDONESIAN RICE GERMPLASM." Indonesian Journal of Agricultural Science 14, no. 2 (October 16, 2013): 71. http://dx.doi.org/10.21082/ijas.v14n2.2013.p71-78.

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A successful molecular breeding program requires detailed and comprehensive understanding of the diversity of rice germ-plasm and genetic base of target traits. The objective of this research was to develop the high throughput 1536-SNP chip linked to heading date and yield component traits and used it for genotyping the diverse Indonesian rice germplasm. The genotype data obtained could be used for diversity analysis and genome wide association mapping study. A 1536-SNP genome wide assay was developed using the Illumina’s GoldenGate technology. The SNP markers were selected in the rice genome regions containing heading date and yield component genes or regions where the quantitative trait loci (QTLs) of the two traits were mapped. The developed custom SNP chips were then used for genotyping 467 rice accessions showing diversity in heading dates and yield components. The assay can reliably be used for diversity analysis and mapping genes associated with heading date and yield component traits. For 1536-SNP BIO-RiceOPA-1 custom chip designed, a total of 34.832 SNPs distributed in rice genome particularly in the region of heading date and yield component genes or QTLs were identified. A total of 1536-SNP were selected and confirmed to be used for genotyping analysis. Analysis performance and quality of 1536-SNP BIO-RiceOPA1 showed that 60% (918/1536) of total SNP markers had a good differentiating power in scanning the rice accessions tested (MAF > 0.2). The 1536-SNP genome wide assay Illumina’s GoldenGate designed was useful for diversity analysis and could be used as SNP marker for large scale genotyping in rice molecular breeding involving Indica-Indica, Indica-Japonica and Indica-Tropical Japonica crosses. <br />

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16

B. Lade, Diksha, Dayanand P. Gogle, and Bipin D. Lade. "Development of Silver Nanoparticles/PEG/Glycerine Composite for Antibacterial Effect using Leaf Extract of Ocimum sanctum and Ocimum basilicum." Volume 4,Issue 5,2018 4, no. 5 (November 12, 2018): 527–32. http://dx.doi.org/10.30799/jnst.161.18040517.

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The main purpose of the experiment is to use green synthesis method for silver nanoparticles (SNP) fabrication using phytochemical and functional groups inherent in aqueous leaf extract of Ocimum sanctum and Ocimum basilicum for formulation of polyethylene glycol (PEG)/ Glycerine film. The SNP synthesis reaction is performed under sun condition and change in colour from light brown to dark brown was the initial indication, observed for nanoparticles synthesis. The 95 mL of 0.001 M AgNO3 is mixed with 5 mL of leaf extract and reaction performed under Sun light at alkaline pH 8 was found efficient to produced stable NP. The synthesized SNP are mixed with (10%, 50%, 100%, 150%, 200% and 250%), polyethylene glycol (PEG):glycerine (G) in 1:1 ratio to form a film. The UV-spectroscopic analysis confirms absorption at 420-430 nm for synthesized SNP. The FTIR characterization determines alkynes (terminal), 1�, 2� amines, amides, nitriles, alkynes, alkyl halides functional group from O. sanctum (OS) leaf extract and aldehydes, alkynes (terminal), alkyne, alkene, from O. basilicum (OB) leaf extract responsible for reducing and capping silver nitrate to form nanoparticles. The SEM analysis verify that the O. sanctum based nanoparticles are spherical in shape although O. basilicum based nanoparticles have bright contrast coral reef like morphology. The average zeta potential of silver nanoparticles was found to be 27.74 mV and 23.50 mV that are embedded in Ocimum sanctum-SNP/PEG and Ocimum basilicum-SNP/PEG films. Also, the average diameters of SNP in Ocimum sanctum-SNP/PEG and in Ocimum basilicum-SNP/PEG was found to be 463.2 nm and 43.0 nm. These Sun light mediated SNP shows antimicrobial activity against E. coli and S. aureous pathogens.

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17

Hsieh, Ming-Hong, Hsueh-Ju Lu, Chiao-Wen Lin, Chia-Yi Lee, Shang-Jung Yang, Pei-Hsuan Wu, Mu-Kuan Chen, and Shun-Fa Yang. "Genetic Variants of lncRNA GAS5 Are Associated with the Clinicopathologic Development of Oral Cancer." Journal of Personalized Medicine 11, no. 5 (April 26, 2021): 348. http://dx.doi.org/10.3390/jpm11050348.

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The long noncoding RNA, Growth arrest-specific 5 (GAS5) plays a crucial role in the development of oral cancer. However, potential genetic variants in GAS5 that affect the susceptibility and progression of oral cancer have rarely been explored. In this study, two loci of GAS5 single nucleotide polymorphisms (SNPs) (rs145204276 and rs55829688) were genotyped by using the TaqMan allelic discrimination in 1125 oral cancer patients and 1195 non-oral-cancer individuals. After statistical analyses, the distribution of both the GAS5 SNP rs145204276 and GAS5 SNP rs55829688 frequencies were similar between the study and control groups. However, the patients with GAS5 SNP rs145204276 variants (Ins/Del or Del/Del) showed a higher tendency of moderate to poor cell differentiation of oral cancer (OR: 1.454, 95% CI: 1.041–2.031, p = 0.028). Moreover, the GAS5 SNP rs145204276 variants (Ins/Del or Del/Del) in the non-alcohol-drinking population were associated with significantly advanced tumor stage (OR: 1.500, 95% CI: 1.081–2.081, p = 0.015) and larger tumor size (OR: 1.494, 95% CI: 1.076–2.074, p = 0.016). Furthermore, individuals with the GAS5 SNP rs145204276 variant were associated with a higher expression of GAS5 in the GTEx database (p = 0.002), and the higher GAS5 level was associated with poor cell differentiation, advanced tumor stage and larger tumor size in head and neck squamous cell carcinoma from the TCGA database (all p < 0.05). In conclusion, the GAS5 SNP rs145204276 variant is related to poor-differentiation cell status in oral cancer. Besides, the presence of the GAS5 SNP rs145204276 variant is associated with a worse tumor stage and tumor size in oral cancer patients without alcohol drinking.

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18

Cervantes-Pérez, Daniela, Angélica Ortega-García, Rigoberto Medina-Andrés, Ramón Alberto Batista-García, and Verónica Lira-Ruan. "Exogenous Nitric Oxide Delays Plant Regeneration from Protoplast and Protonema Development in Physcomitrella patens." Plants 9, no. 10 (October 16, 2020): 1380. http://dx.doi.org/10.3390/plants9101380.

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Nitric oxide (NO) has been recognized as a major player in the regulation of plant physiology and development. NO regulates cell cycle progression and cell elongation in flowering plants and green algae, although the information about NO function in non-vascular plants is scarce. Here, we analyze the effect of exogenous NO on Physcomitrella patens protonema growth. We find that increasing concentrations of the NO donor sodium nitroprusside (SNP) inhibit protonema relative growth rate and cell length. To further comprehend the effect of NO on moss development, we analyze the effect of SNP 5 and 10 µM on protoplast regeneration and, furthermore, protonema formation compared with untreated plants (control). Isolated protoplasts were left to regenerate for 24 h before starting the SNP treatments that lasted five days. The results show that SNP restrains the protoplast regeneration process and the formation of new protonema cells. When SNP treatments started five days after protoplast isolation, a decrease in cell number per protonema filament was observed, indicating an inhibition of cell cycle progression. Our results show that in non-vascular plants, NO negatively regulates plant regeneration, cell cycle and cell elongation.

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19

Chen, Jianguo, Driguneswar Pinnamaneni, Shravan Komaragiri, Cherrelle Wright, and Briauna Hawthorne. "Selecting Cell Lines for SNP Human Identification Assay Development." Atlas Journal of Biotechnology 1, no. 1 (January 1, 2011): 21–26. http://dx.doi.org/10.5147/ajbtch.2011.0026.

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20

Lapègue, S., E. Harrang, S. Heurtebise, E. Flahauw, C. Donnadieu, P. Gayral, M. Ballenghien, et al. "Development of SNP-genotyping arrays in two shellfish species." Molecular Ecology Resources 14, no. 4 (March 5, 2014): 820–30. http://dx.doi.org/10.1111/1755-0998.12230.

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21

Labate, Joanne A., Jeffrey C. Glaubitz, and Michael J. Havey. "Genotyping by sequencing for SNP marker development in onion." Genome 63, no. 12 (December 2020): 607–13. http://dx.doi.org/10.1139/gen-2020-0011.

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Onion (Allium cepa) is not highly tractable for development of molecular markers due to its large (16 gigabases per 1C) nuclear genome. Single nucleotide polymorphisms (SNPs) are useful for genetic characterization and marker-aided selection of onion because of codominance and common occurrence in elite germplasm. We completed genotyping by sequencing (GBS) to identify SNPs in onion using 46 F2 plants, parents of the F2 plants (Ailsa Craig 43 and Brigham Yellow Globe 15-23), two doubled haploid (DH) lines (DH2107 and DH2110), and plants from 94 accessions in the USDA National Plant Germplasm System (NPGS). SNPs were called using the TASSEL 3.0 Universal Network Enabled Analysis (UNEAK) bioinformatics pipeline. Sequences from the F2 and DH plants were used to construct a pseudo-reference genome against which genotypes from all accessions were scored. Quality filters were used to identify a set of 284 high quality SNPs, which were placed onto an existing genetic map for the F2 family. Accessions showed a moderate level of diversity (mean He = 0.341) and evidence of inbreeding (mean F = 0.592). GBS is promising for SNP discovery in onion, although lack of a reference genome required extensive custom scripts for bioinformatics analyses to identify high quality markers.

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22

Li, X. P., Z. L. Hu, S. J. Moon, K. T. Do, Y. K. Ha, H. Kim, M. J. Byun, et al. "Development of anin silicocoding gene SNP map in pigs." Animal Genetics 39, no. 4 (August 2008): 446–50. http://dx.doi.org/10.1111/j.1365-2052.2008.01727.x.

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23

Senge, T., A. Junge, and B. Madea. "The development of three SNP assays for forensic casework." International Congress Series 1288 (April 2006): 46–48. http://dx.doi.org/10.1016/j.ics.2005.09.019.

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24

Ma, Jiejie, Renxiao Zhang, Wei Zhao, Li Zhao, Mingrui Zhou, Tingsen Jing, and Hui Luo. "SNP marker development and polymorphism detection of Schizothorax waltoni." Conservation Genetics Resources 12, no. 2 (April 27, 2019): 199–203. http://dx.doi.org/10.1007/s12686-019-01096-w.

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25

Pakull, Birte, Lasse Schindler, Malte Mader, Birgit Kersten, Celine Blanc-Jolivet, Maike Paulini, Maristerra R. Lemes, et al. "Development of nuclear SNP markers for Mahogany (Swietenia spp.)." Conservation Genetics Resources 12, no. 4 (August 12, 2020): 585–87. http://dx.doi.org/10.1007/s12686-020-01162-8.

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Abstract Swietenia species are the most valuable American tropical timbers and have been heavily overexploited for decades. The three species are listed as either vulnerable or endangered by IUCN and are included on Appendix II of CITES, yet illegal exploitation continues. Here, we used restriction associated DNA sequencing to develop a new set of 120 SNP markers for Swietenia sp., suitable for MassARRAY®iPLEX™ genotyping. These markers can be used for population genetic studies and timber tracking purposes.

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26

Augustinus, Daniel, Michelle E. Gahan, and Dennis McNevin. "Development of a forensic identity SNP panel for Indonesia." International Journal of Legal Medicine 129, no. 4 (August 8, 2014): 681–91. http://dx.doi.org/10.1007/s00414-014-1055-4.

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27

Wang, L., W. He, J. Mao, H. Wang, B. Jin, H. B. Luo, W. B. Liang, and L. Zhang. "Development of a SNP-STRs multiplex for forensic identification." Forensic Science International: Genetics Supplement Series 5 (December 2015): e598-e600. http://dx.doi.org/10.1016/j.fsigss.2015.09.236.

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Kersten, Birgit, Mina Merle Voss, and Matthias Fladung. "Development of mitochondrial SNP markers in different Populus species." Trees 29, no. 2 (December 19, 2014): 575–82. http://dx.doi.org/10.1007/s00468-014-1136-5.

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29

Byers, Robert L., David B. Harker, Scott M. Yourstone, Peter J. Maughan, and Joshua A. Udall. "Development and mapping of SNP assays in allotetraploid cotton." Theoretical and Applied Genetics 124, no. 7 (January 18, 2012): 1201–14. http://dx.doi.org/10.1007/s00122-011-1780-8.

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30

Viana, K. S., M. C. C. Bussiere, C. S. Paes de Carvalho, B. L. Dias, M. R. Faes, V. R. Lanes, C. R. Quirino, and R. C. M. Escobar. "359 MORPHOLOGIC AND BIOCHEMISTRY ALTERATIONS ON BOVINE OOCYTE MATURATION IN VITRO WITH NITRIC OXIDE AND ITS IMPACT ON EMBRYO DEVELOPMENT." Reproduction, Fertility and Development 22, no. 1 (2010): 336. http://dx.doi.org/10.1071/rdv22n1ab359.

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The aim of this study was to evaluate morphologic and biochemistry alterations caused by the addition of sodium nitroprusside (SNP), a NO donor, on bovine oocyte maturation in vitro. Bovine ovaries were collected at a local abattoir. COC were cultured in TCM-199 with 10% FCS, 0.5 μg mL-1 FSH, 5.0 μg mL-1 LH, and antibiotics. Analysis of variance was conducted and the means were compared by t-test at a level of 5%. Experimental design: (1) evaluation of the oocyte plasma membrane viability and integrity using Annexin V/propidium iodide (PI) and Hoechst 33342/PI staining, respectively; (2) microtubule and microfilament organization, and migration of cortical granules by immunofluorescence; (3) oocyte glutathione content and concentration of NO3-/NO2-using the method of Griess (Ricart-Jane D et al. 2002 Nitric Oxide 6, 178-185) and (4) embryo development. In Experiment 1, the addition of 1 mM SNP caused cellular death in the majority of the oocytes [100%, AnnexinV/PI (+) and 80.7% Hoescht/IP (+)] differing from the control group and the 0.01 mM SNP (P < 0.05). In Experiment 2, the microtubule staining was observed in the cytoplasm in both control group and 0.01 mM SNP; however, the group treated with 1 mM of SNP exhibited clear defects in spindle and chromatin arrangements (P < 0.05). No alterations in microfilaments disposition was observed in the control group and 0.01 mM SNP. However, after the addition of 1 mM, the microfilaments arranged into clusters, and not below of the cortex. Oocytes treated with 1 mM SNP (68.2%) showed total cortical granule migration to the periphery of the ooplasm and were similar to the control group (72.2%) (P > 0.05). Nevertheless, in the group treated with 0.01 mM SNP the total cortical granule migration was greater (86.8%, P < 0.05). In Experiment 3, the glutathione content of oocytes cultured in the presence of 1 mM SNP was lower (4.4p mol) when compared to the control group (5.4p mol) and 0.01 mM SNP (5.5 pmol) (P > 0.05). The concentration of NO in the medium were similar to both control group (6.0 ± 3.0 μM) and treated with 0.01 mM SNP (15.8 ± 1.9 μM), however, the treatment with 1 mM SNP increased 10 times (59.9 ± 12.0 μM; P < 0.05) this concentration. In Experiment 4, cleavage rates and embryo development were similar for groups control and 0.01 mM SNP (P > 0.05). Even so, in the group treated with 0.01 mM there was a greater blastocyst cell number when compared to the control group (256.8 ± 52.5 and 196.9 ± 54.0, respectively-P < 0.05). These results indicate that: (1) the addition of 0.01 mM SNP increased the quality of the oocyte maturation, leading to a higher percentage of cortical granules migration and blastocyst cell numbers, in a different pathway from that of glutathione; (2) the addition of 1 mM of SNP caused a cytotoxic effect, leading to cellular death with loss of viability and integrity of plasma membrane, absence of nuclear maturation/organization of cytoskeleton and reduction of the glutathione content, although with no intervention in the migration of cortical granules.

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31

Jenkins, Suzanne, and Neil Gibson. "High-Throughput SNP Genotyping." Comparative and Functional Genomics 3, no. 1 (2002): 57–66. http://dx.doi.org/10.1002/cfg.130.

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Whole genome approaches using single nucleotide polymorphism (SNP) markers have the potential to transform complex disease genetics and expedite pharmacogenetics research. This has led to a requirement for high-throughput SNP genotyping platforms. Development of a successful high-throughput genotyping platform depends on coupling reliable assay chemistry with an appropriate detection system to maximise efficiency with respect to accuracy, speed and cost. Current technology platforms are able to deliver throughputs in excess of 100 000 genotypes per day, with an accuracy of >99%, at a cost of 20–30 cents per genotype. In order to meet the demands of the coming years, however, genotyping platforms need to deliver throughputs in the order of one million genotypes per day at a cost of only a few cents per genotype. In addition, DNA template requirements must be minimised such that hundreds of thousands of SNPs can be interrogated using a relatively small amount of genomic DNA. As such, it is predicted that the next generation of high-throughput genotyping platforms will exploit large-scale multiplex reactions and solid phase assay detection systems.

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32

Kumar, Manish, D. P. Bhadoria, Koushik Dutta, Mitesh Kumar F., Bharat Singh, Seema Singh, Anil K. Chhillar, D. Behera, and G. L. Sharma. "Theα1ATandTIMP-1Gene Polymorphism in the Development of Asthma." Comparative and Functional Genomics 2012 (2012): 1–10. http://dx.doi.org/10.1155/2012/968267.

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Asthma has been an inflammatory disorder accompanied by tissue remodeling and protease-antiprotease imbalance in lungs. The SNPs ofalpha-1 antitrypsin(α1AT) andtissue inhibitor of metalloproteinase-1(TIMP-1) genes were studied for their association with asthma. Genotyping ofα1ATandTIMP-1genes was performed in 202 asthmatics and 204 controls. Serum levels ofα1AT, TIMP-1 and cytokines were estimated to find if the interplay between genotypes and cellular biomarkers determines the pathogenesis of asthma. The analysis of results showed significantly low level ofα1AT in the serum of asthmatics as compared to controls (P=0.001), whereas cytokines were elevated in patients. No significant difference was observed in the concentration of TIMP-1 in patients and controls. Genotyping led to the identification of 3 SNPs (Val213Ala, Glu363Lys, and Glu376Asp) inα1ATgene. The novel SNP Glu363Lys ofα1ATwas found to be associated with asthma (P=0.001). The analysis ofTIMP-1gene showed the occurrence of seven SNPs, including a novel intronic SNP at base G3774A. The allele frequency of G3774A and Phe124Phe was significantly higher in asthmatics as compared to controls. Thus, the SNP Glu363Lys ofα1ATand G3774A and Phe124Phe ofTIMP-1could be important genetic markers for use in better management of the disease.

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33

Mahabir, Amrita, Lambert A. Motilal, David Gopaulchan, Saila Ramkissoon, Antoinette Sankar, and Pathmanathan Umaharan. "Development of a core SNP panel for cacao (Theobroma cacao L.) identity analysis." Genome 63, no. 2 (February 2020): 103–14. http://dx.doi.org/10.1139/gen-2019-0071.

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Single nucleotide polymorphisms (SNPs) are preferred markers for DNA fingerprinting and diversity studies in cacao (Theobroma cacao L.). Yet, a consensus SNP panel with a minimum number of SNPs for optimal identity analysis is unavailable for cacao. An initial set of 146 SNP panels of varying sizes were assembled based on heterozygosity, linkage disequilibrium (LD), linkage group (LG) distribution, major allele frequency, minor allele frequency (MiAF), polymorphism information content (PIC), and random distribution. These panels were assessed to determine their ability to distinguish among a training set of 155 accessions. The panels with the best separation ability were supplemented with additional SNPs to create 16 designer panels, which separated all 155 accessions. The 16 designer SNP panels were then assessed on a dataset of 1220 accessions coming from 10 ancestral groups. Increasing the number of SNPs generally yielded improved resolution of genetic identities with concomitant reduction of synonymous groups. The number and choice of SNPs were critical factors with LD, MiAF, and PIC being important selection attributes but an even LG distribution was unnecessary. A robust set of 96 SNPs is recommended as a minimal core SNP panel for cacao DNA fingerprinting to the international cacao community.

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34

Barnes, Michael R. "SNP and Mutation Data on the Web – Hidden Treasures for Uncovering." Comparative and Functional Genomics 3, no. 1 (2002): 67–74. http://dx.doi.org/10.1002/cfg.131.

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SNP data has grown exponentially over the last two years, SNP database evolution has matched this growth, as initial development of several independent SNP databases has given way to one central SNP database, dbSNP. Other SNP databases have instead evolved to complement this central database by providing gene specific focus and an increased level of curation and analysis on subsets of data, derived from the central data set. By contrast, human mutation data, which has been collected over many years, is still stored in disparate sources, although moves are afoot to move to a similar central database. These developments are timely, human mutation and polymorphism data both hold complementary keys to a better understanding of how genes function and malfunction in disease. The impending availability of a complete human genome presents us with an ideal framework to integrate both these forms of data, as our understanding of the mechanisms of disease increase, the full genomic context of variation may become increasingly significant.

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35

Shang, Junliang, Yan Sun, Shengjun Li, Jin-Xing Liu, Chun-Hou Zheng, and Junying Zhang. "An Improved Opposition-Based Learning Particle Swarm Optimization for the Detection of SNP-SNP Interactions." BioMed Research International 2015 (2015): 1–12. http://dx.doi.org/10.1155/2015/524821.

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SNP-SNP interactions have been receiving increasing attention in understanding the mechanism underlying susceptibility to complex diseases. Though many works have been done for the detection of SNP-SNP interactions, the algorithmic development is still ongoing. In this study, an improved opposition-based learning particle swarm optimization (IOBLPSO) is proposed for the detection of SNP-SNP interactions. Highlights of IOBLPSO are the introduction of three strategies, namely, opposition-based learning, dynamic inertia weight, and a postprocedure. Opposition-based learning not only enhances the global explorative ability, but also avoids premature convergence. Dynamic inertia weight allows particles to cover a wider search space when the considered SNP is likely to be a random one and converges on promising regions of the search space while capturing a highly suspected SNP. The postprocedure is used to carry out a deep search in highly suspected SNP sets. Experiments of IOBLPSO are performed on both simulation data sets and a real data set of age-related macular degeneration, results of which demonstrate that IOBLPSO is promising in detecting SNP-SNP interactions. IOBLPSO might be an alternative to existing methods for detecting SNP-SNP interactions.

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36

Lott, Timothy J., and Robin T. Scarborough. "Development of a MLST-biased SNP microarray for Candida albicans." Fungal Genetics and Biology 45, no. 6 (June 2008): 803–11. http://dx.doi.org/10.1016/j.fgb.2008.01.005.

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37

Cheong, H. S., L. H. Kim, S. Namgoong, and H. D. Shin. "Development of discrimination SNP markers for Hanwoo (Korean native cattle)." Meat Science 94, no. 3 (July 2013): 355–59. http://dx.doi.org/10.1016/j.meatsci.2013.03.014.

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38

Baniecki, Mary Lynn, Jade Moon, Kian Sani, Jacob E. Lemieux, Stephen F. Schaffner, and Pardis C. Sabeti. "Development of a SNP barcode to genotype Babesia microti infections." PLOS Neglected Tropical Diseases 13, no. 3 (March 25, 2019): e0007194. http://dx.doi.org/10.1371/journal.pntd.0007194.

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39

Terakami, S., C. Nishitani, and T. Yamamoto. "DEVELOPMENT OF SNP MARKERS FOR MARKER-ASSISTED SELECTION IN PEAR." Acta Horticulturae, no. 976 (February 2013): 463–69. http://dx.doi.org/10.17660/actahortic.2013.976.65.

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40

Close, Timothy J., Prasanna R. Bhat, Stefano Lonardi, Yonghui Wu, Nils Rostoks, Luke Ramsay, Arnis Druka, et al. "Development and implementation of high-throughput SNP genotyping in barley." BMC Genomics 10, no. 1 (2009): 582. http://dx.doi.org/10.1186/1471-2164-10-582.

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41

Hyten, David L., Qijian Song, Edward W. Fickus, Charles V. Quigley, Jong-Sung Lim, Ik-Young Choi, Eun-Young Hwang, Marcial Pastor-Corrales, and Perry B. Cregan. "High-throughput SNP discovery and assay development in common bean." BMC Genomics 11, no. 1 (2010): 475. http://dx.doi.org/10.1186/1471-2164-11-475.

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42

Zwan, H., C. Visser, M. Schoonen, and R. van der Sluis. "Development of an SNP ‐based parentage verification panel for lovebirds." Animal Genetics 50, no. 6 (October 3, 2019): 764–67. http://dx.doi.org/10.1111/age.12859.

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43

Peng, Xinliang, Liangjie Zhao, Jun Liu, and Xusheng Guo. "Development of SNP markers for Xenocypris argentea based on transcriptomics." Conservation Genetics Resources 10, no. 4 (October 20, 2017): 679–84. http://dx.doi.org/10.1007/s12686-017-0900-4.

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Yu, Aiqing, Yonghai Shi, and Yinlong Yan. "Development and characterization of 50 SNP markers in Coilia ectenes." Conservation Genetics Resources 12, no. 2 (February 7, 2019): 177–81. http://dx.doi.org/10.1007/s12686-019-01086-y.

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45

Qu, Jiangyong, Shanshan Wang, Yutong Cui, Xiaoyu Guo, and Yunhui Wang. "Development and characterization of 26 SNP markers in Nipponacmea schrenckii." Conservation Genetics Resources 12, no. 2 (May 9, 2019): 195–98. http://dx.doi.org/10.1007/s12686-019-01095-x.

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46

Taylor, U., W. Garrels, S. Petersen, S. Barcikowski, S. Klein, W. Kues, A. Lucas-Hahn, H. Niemann, and D. Rath. "164 DEVELOPMENT OF MURINE EMBRYOS AFTER INJECTION OF UNCOATED GOLD AND SILVER NANOPARTICLES." Reproduction, Fertility and Development 22, no. 1 (2010): 240. http://dx.doi.org/10.1071/rdv22n1ab164.

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Novel techniques such as ultrashort pulsed laser technology to produce in situ bio-conjugated nanoparticles (NP) as biomarkers for optical imaging and intervention hold great potential to observe dynamic processes in gametes and embryos without affecting their developmental potential. With regard to toxicology, current preliminary evidence is mainly based on specific cell lines and suggests low toxicity for gold NP (GNP), but a higher toxicity for silver NP (SNP), which also possess a considerable antibacterial effect. Little is known about their impact on sensitive biological systems as early mammalian embryos. The present study investigated the potential toxicity of GNP and SNP in murine embryos for the first time. Since the NP were laser-generated, they formed a stable dispersion in water without the need of surface coating, which might have caused additional toxic effects. Approximately 10 pL of a NP díspersion (average NP diameter of 15 nm) containing 50 μg mL-1 of either GNP or SNP were injected into 1 blastomere of 2-cell-stage embryos (n = 93 or 75, respectively), derived from superovulated NMRI mice. Embryos injected with water alone (n = 79) served as controls. Untreated embryos (n = 92) were run as a handling control. Successful NP injection was confirmed using laser scanning confocal microscopy. After treatment, embryos were cultured for 72 h at 37°C and 5% CO2 in KSOM plus 1% BSA. Embryo development was assessed on a daily basis. No abnormal development was observed. The handling controls reached a blastocyst rate of 77.2%. A total of 66.2% of the water-injected embryos developed to blastocysts, compared to 62.4% and 56.0% after injection of GNP and SNP, respectively. Neither 1-way ANOVA nor an additional chi-square test indicated significant differences between treatment groups. In conclusion, these preliminary data indicate that intracytoplasmatic injection of GNP and SNP had no significant impact on embryo development. Further tests, including qRT-PCR of development-relevant genes in blastocysts and transfer of injected embryos into recipient animals to study potential long-term effects, are underway to gain a better understanding of GNP and SNP embryo toxicology. We gratefully acknowledge the support of the Masterrind GmbH Verden and the NBank Niedersachsen.

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47

Winfield, Mark, Amanda Burridge, Matthew Ordidge, Helen Harper, Paul Wilkinson, Danny Thorogood, Liz Copas, Keith Edwards, and Gary Barker. "Development of a minimal KASP marker panel for distinguishing genotypes in apple collections." PLOS ONE 15, no. 11 (November 30, 2020): e0242940. http://dx.doi.org/10.1371/journal.pone.0242940.

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Accurate identification of named accessions in germplasm collections is extremely important, especially for vegetatively propagated crops which are expensive to maintain. Thus, an inexpensive, reliable, and rapid genotyping method is essential because it avoids the need for laborious and time-consuming morphological comparisons. Single Nucleotide Polymorphism (SNP) marker panels containing large numbers of SNPs have been developed for many crop species, but such panels are much too large for basic cultivar identification. Here, we have identified a minimum set of SNP markers sufficient to distinguish apple cultivars held in the English and Welsh national collections providing a cheaper and automatable alternative to the markers currently used by the community. We show that SNP genotyping with a small set of well selected markers is equally efficient as microsatellites for the identification of apple cultivars and has the added advantage of automation and reduced cost when screening large numbers of samples.

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48

Gao, H. J., and H. Q. Yang. "Nitric oxide effect on root architecture development in Malus seedlings." Plant, Soil and Environment 57, No. 9 (August 30, 2011): 418–22. http://dx.doi.org/10.17221/209/2011-pse.

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 The time-dependent production of nitric oxide (NO) in roots induced by indole-3-butyric acid (IBA) and the effect of sodium nitroprusside (SNP) on root architecture development were investigated, using Malus hupehensis Rehd. seedlings. Following IBA application, a very rapid increase in NO formation and a subsequent second wave of NO burst was observed, which was related to the induction of lateral roots (LRs) and the organogenesis of lateral root primordia (LRP), respectively. The first NO burst was correlated with the second and the two peaks of NO burst induced by IBA were totally abolished by 3,3’,4’,5,7-pentahydroxyflavone (quercetin). Exogenous NO promoted the emergence and elongation of LR and inhibited the elongation of primary root (PR) in a dose-dependent manner: low concentrations of SNP promoted both the amounts and the elongation of LR but inhibited the elongation of LR and PR at higher concentrations. It was concluded that (i) the rapid production of NO induced by IBA was correlated with the IBA-induced initiation of LR; (ii) quercetin inhibition of IBA-induced LR formation was correlated with the quercetin inhibition of IBA-induced NO biosynthesis, and (iii) exogenous NO affects the development of root system architecture in a dose-dependent manner.

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49

Xiao, Shijun, Panpan Wang, Linsong Dong, Yaguang Zhang, Zhaofang Han, Qiurong Wang, and Zhiyong Wang. "Whole-genome single-nucleotide polymorphism (SNP) marker discovery and association analysis with the eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA) content inLarimichthys crocea." PeerJ 4 (December 21, 2016): e2664. http://dx.doi.org/10.7717/peerj.2664.

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Whole-genome single-nucleotide polymorphism (SNP) markers are valuable genetic resources for the association and conservation studies. Genome-wide SNP development in many teleost species are still challenging because of the genome complexity and the cost of re-sequencing. Genotyping-By-Sequencing (GBS) provided an efficient reduced representative method to squeeze cost for SNP detection; however, most of recent GBS applications were reported on plant organisms. In this work, we used anEcoRI-NlaIII based GBS protocol to teleost large yellow croaker, an important commercial fish in China and East-Asia, and reported the first whole-genome SNP development for the species. 69,845 high quality SNP markers that evenly distributed along genome were detected in at least 80% of 500 individuals. Nearly 95% randomly selected genotypes were successfully validated by Sequenom MassARRAY assay. The association studies with the muscle eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA) content discovered 39 significant SNP markers, contributing as high up to ∼63% genetic variance that explained by all markers. Functional genes that involved in fat digestion and absorption pathway were identified, such asAPOB,CRATandOSBPL10. Notably,PPT2Gene, previously identified in the association study of the plasma n-3 and n-6 polyunsaturated fatty acid level in human, was re-discovered in large yellow croaker. Our study verified thatEcoRI-NlaIII based GBS could produce quality SNP markers in a cost-efficient manner in teleost genome. The developed SNP markers and the EPA and DHA associated SNP loci provided invaluable resources for the population structure, conservation genetics and genomic selection of large yellow croaker and other fish organisms.

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Serveaux-Dancer, Marine, Matthieu Jabaudon, Isabelle Creveaux, Corinne Belville, Raïko Blondonnet, Christelle Gross, Jean-Michel Constantin, Loïc Blanchon, and Vincent Sapin. "Pathological Implications of Receptor for Advanced Glycation End-Product (AGER) Gene Polymorphism." Disease Markers 2019 (February 4, 2019): 1–17. http://dx.doi.org/10.1155/2019/2067353.

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The receptor for advanced glycation end-products (RAGE) is a cell surface transmembrane multiligand receptor, encoded by the AGER gene. RAGE presents many transcripts, is expressed mainly in the lung, and involves multiple pathways (such as NFκB, Akt, p38, and MAP kinases) that initiate and perpetuate an unfavorable proinflammatory state. Due to these numerous functional activities, RAGE is implicated in multiple diseases. AGER is a highly polymorphic gene, with polymorphisms or SNP (single-nucleotide polymorphism) that could be responsible or co-responsible for disease development. This review was designed to shed light on the pathological implications of AGER polymorphisms. Five polymorphisms are described: rs2070600, rs1800624, rs1800625, rs184003, and a 63 bp deletion. The rs2070600 SNP may be associated with the development of human autoimmune disease, diabetes complications, cancer, and lung diseases such as chronic obstructive pulmonary disease and acute respiratory distress syndrome. The rs1800624 SNP involves AGER gene regulation and may be related to reduced risk of heart disease, cancer, Crohn’s disease, and type 1 diabetes complications. The rs1800625 SNP may be associated with the development of diabetic retinopathy, cancer, and lupus but may be protective against cardiovascular risk. The rs184003 SNP seems related to coronary artery disease, breast cancer, and diabetes. The 63 bp deletion may be associated with reduced survival from heart diseases during diabetic nephropathy. Here, these potential associations between AGER polymorphisms and the development of diseases are discussed, as there have been conflicting findings on the pathological impact of AGER SNPs in the literature. These contradictory results might be explained by distinct AGER SNP frequencies depending on ethnicity.

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