SNPs Detection and Genetic Analysis of Chionanthus retusus via Genotyping-by-Sequencing
References
- Chang MC, Qiu L, Green P (1996) Oleaceae. Flora of China 15, 272-319.
- Duke J, Wain K (1981) Medicinal plants of the world. Computer index with more than 85000 entries. Handbook of Medicinal Herbs CRC press Florida, Boca Raton. 96.
- Huxley A (1992) New RHS dictionary of gardening 1: 203–205. acmillan ISBN 0-333-47494-5.
- Lee YG, Lee H, Jung JW, Seo KH, Lee DY, Kim HG, Ko JH, Lee DS, Baek NI (2019) Flavonoids from Chionanthus retusus (Oleaceae) Flowers and Their Protective Effects against Glutamate-Induced Cell Toxicity in HT22 Cells. International journal of molecular sciences. 20(14):3517. https://doi.org/10.3390/ijms20143517
- Gülçin İ, Elias R, Gepdiremen A, Taoubi K, Köksal E (2009) Antioxidant secoiridoids from fringe tree (Chionanthus virginicus L.). Wood science and technology. 43(3-4):195. https://doi.org/10.1007/s00226-008-0234-1
- Kwak JH, Kang MW, Roh JH, Choi SU, Zee OP (2009) Cytotoxic phenolic compounds from Chionanthus retusus. Archives of pharmacal research. 32(12):1681-1687. https://doi.org/10.1007/s12272-009-2203-0
- Kim M-S, Lee E-H, Cho Y-J (2015) Anti-oxidative Activities of Extracts from Chionanthus retusus leaves, Fruits and FLower. Current Research on Agriculture and Life Sciences. 33(2):49-56.
- Hu X-l, Jiang Q, Yin F-j, Liu T (2010) Extraction and Determination of Mineral Elements and Bioactive Components in Chinese Fringe Tree Young Leaf Tea and Flower Tea [J]. Food Science. 18.
- Kim KS, Lee YH, Jang YS, Choi IH (2013) Analysis of fatty acid compositions and biodiesel properties of seeds of woody oil plants in Korea. Korean Journal of Plant Resources. 26(5):628-635. https://doi.org/10.7732/kjpr.2013.26.5.628
- Gao J, Yin W (2016) Flower Essential Oil Composition of Chionanthus retusus. Chemistry of Natural Compounds. 52(5):934-935. https://doi.org/10.1007/s10600-016-1823-0
- Soejima A, Maki M, Ueda K (1998) Genetic variation in relic and isolated populations of Chionanthus retusus (Oleaceae) of Tsushima Island and the Tôno region, Japan. Genes & genetic systems. 73(1):29-37.
- He Y, Liu L, Yang S, Dong M, Yuan W, Shang F (2017) Characterization of the complete chloroplast genome of Chinese fringetree (Chionanthus retusus). Conservation genetics resources. 9(3):431-434. https://doi.org/10.1007/s12686-017-0704-6
- Wang Z, Tanksley S (1989) Restriction fragment length polymorphism in Oryza sativa L. Genome. 32(6):1113-1118. https://doi.org/10.1139/g89-563
- Lanteri S, Saba E, Cadinu M, Mallica G, Baghino L, Portis E (2004) Amplified fragment length polymorphism for genetic diversity assessment in globe artichoke. Theoretical and Applied Genetics. 108(8):1534-1544. https://doi.org/10.1007/s00122-003-1576-6
- Smith J, Kresovich S, Hopkins M, Mitchell S, Dean R, Woodman W, Lee M, Porter K (2000) Genetic diversity among elite sorghum inbred lines assessed with simple sequence repeats. Crop Science. 40(1):226-232. https://doi.org/10.2135/cropsci2000.401226x
- Etter PD, Bassham S, Hohenlohe PA, Johnson EA, Cresko WA (2012) SNP discovery and genotyping for evolutionary genetics using RAD sequencing. Molecular methods for evolutionary genetics. Springer; p. 157-178. https://doi.org/10.1007/978-1-61779-228-1_9
- Pegadaraju V, Nipper R, Hulke B, Qi L, Schultz Q (2013) De novo sequencing of sunflower genome for SNP discovery using RAD (Restriction site Associated DNA) approach. BMC genomics. 14(1):556. https://doi.org/10.1186/1471-2164-14-556
- Porebski S, Bailey LG, Baum BR (1997) Modification of a CTAB DNA extraction protocol for plants containing high polysaccharide and polyphenol components. Plant molecular biology reporter. 15(1):8-15. https://doi.org/10.1007/bf02772108
- Baird NA, Etter PD, Atwood TS, Currey MC, Shiver AL, Lewis ZA, Selker EU, Cresko WA, Johnson EA (2008) Rapid SNP discovery and genetic mapping using sequenced RAD markers. PloS one. 3(10):e3376. https://doi.org/10.1371/journal.pone.0003376
- Li H, Durbin R (2009) Fast and accurate short read alignment with Burrows– Wheeler transform. bioinformatics. 25(14):1754-1760. https://doi.org/10.1093/bioinformatics/btp324
- Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R (2009) The sequence alignment/map format and SAMtools. Bioinformatics. 25(16):2078-2079. https://doi.org/10.1093/bioinformatics/btp352
- Danecek P, Auton A, Abecasis G, Albers CA, Banks E, DePristo MA, Handsaker RE, Lunter G, Marth GT, Sherry ST, McVean G, Durbin R (2011) The variant call format and VCFtools. Bioinformatics. 27(15):2156-2158. https://doi.org/10.1093/bioinformatics/btr330
- Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira MA, Bender D, Maller J, Sklar P, De Bakker PI, Daly MJ (2007) PLINK: a tool set for whole-genome association and population-based linkage analyses. The American journal of human genetics. 81(3):559-575. https://doi.org/10.1086/519795
- Yang J, Lee SH, Goddard ME, Visscher PM (2011) GCTA: a tool for genome-wide complex trait analysis. The American Journal of Human Genetics. 88(1):76-82. https://doi.org/10.1016/j.ajhg.2010.11.011
- Excoffier L, Lischer HE (2010) Arlequin suite ver 3.5: a new series of programs to perform population genetics analyses under Linux and Windows. Molecular ecology resources. 10(3):564-567. https://doi.org/10.1111/j.1755-0998.2010.02847.x
- Sonah H, Bastien M, Iquira E, Tardivel A, Légaré G, Boyle B, Normandeau É, Laroche J, Larose S, Jean M (2013) An improved genotyping by sequencing (GBS) approach offering increased versatility and efficiency of SNP discovery and genotyping. PloS one. 8(1):e54603. https://doi.org/10.1371/journal.pone.0054603
- Wang Y, Ning Z, Hu Y, Chen J, Zhao R, Chen H, Ai N, Guo W, Zhang T (2015) Molecular mapping of restriction-site associated DNA markers in allotetraploid upland cotton. PLoS One. 10(4):e0124781. https://doi.org/10.1371/journal.pone.0124781
- Baxter SW, Davey JW, Johnston JS, Shelton AM, Heckel DG, Jiggins CD, Blaxter ML (2011) Linkage mapping and comparative genomics using next-generation RAD sequencing of a non-model organism. PloS one. 6(4):e19315. https://doi.org/10.1371/journal.pone.0019315
- Berthouly-Salazar C, Mariac C, Couderc M, Pouzadoux J, Floc’h J-B, Vigouroux Y (2016) Genotyping-by-sequencing SNP identification for crops without a reference genome: using transcriptome based mapping as an alternative strategy. Frontiers in plant science. 7:777. https://doi.org/10.3389/fpls.2016.00777
- Baali-Cherif D, Besnard G (2005) High genetic diversity and clonal growth in relict populations of Olea europaea subsp laperrinei (Oleaceae) from Hoggar, Algeria. ANNALS OF BOTANY,2005, 96(5): 823-830. https://doi.org/10.1093/aob/mci232
- Nelson MR, Marnellos G, Kammerer S, Hoyal CR, Shi MM, Cantor CR, Braun A (2004) Large-scale validation of single nucleotide polymorphisms in gene regions. Genome research. 14(8):1664-1668. https://doi.org/10.1101/gr.2421604
- Nielsen R (2005) Molecular signatures of natural selection. Annu Rev Genet. 39, 197-218. https://doi.org/10.1146/annurev.genet.39.073003.112420
- Ma B, Liao L, Peng Q, Fang T, Zhou H, Korban SS, Han Y (2017) Reduced representation genome sequencing reveals patterns of genetic diversity and selection in apple. Journal of integrative plant biology. 59(3):190-204. https://doi.org/10.1111/jipb.12522
- Xue X.J, Du XY, Gai Y, Tang Y, Sun YX, Song LQ, Jiang ZW (2020) Application progress of SNPs in plants based on GBS sequencing. 48, 62-68. DOI:10.15889/j. issn.1002-1302.2020.13.012
- Niu SZ, Song QF, Koiwa H, et al. (2019) Genetic diversity, linkage disequilibrium, and population structure analysis of the tea plant (Camellia sinensis) from an origin center, Guizhou plateau, using genome-wide SNPs developed by genotyping-by-sequencing. BMC Plant Biology19, 328. https://doi.org/10.1186/s12870-019-1917-5
Language: English
Page range: 118 - 125
Published on: Jul 16, 2023
Published by: Johann Heinrich von Thünen Institute
In partnership with: Paradigm Publishing Services
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© 2023 Song Huang, Wei Zheng, Xiangpeng Liang, Qingda Duan, Juan Wang, Yaoqing Sun, Tianxiao Ma, published by Johann Heinrich von Thünen Institute
This work is licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 3.0 License.