SNPs Detection and Genetic Analysis of Chionanthus retusus via Genotyping-by-Sequencing

Chang MC, Qiu L, Green P (1996) Oleaceae. Flora of China 15, 272-319. Search in Google Scholar

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. Search in Google Scholar

Huxley A (1992) New RHS dictionary of gardening 1: 203–205. acmillan ISBN 0-333-47494-5. Search in Google Scholar

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 Search in Google Scholar

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 Search in Google Scholar

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 Search in Google Scholar

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. Search in Google Scholar

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. Search in Google Scholar

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 Search in Google Scholar

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 Search in Google Scholar

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. Search in Google Scholar

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 Search in Google Scholar

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 Search in Google Scholar

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 Search in Google Scholar

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 Search in Google Scholar

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 Search in Google Scholar

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 Search in Google Scholar

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 Search in Google Scholar

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 Search in Google Scholar

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 Search in Google Scholar

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 Search in Google Scholar

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 Search in Google Scholar

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 Search in Google Scholar

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 Search in Google Scholar

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 Search in Google Scholar

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 Search in Google Scholar

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 Search in Google Scholar

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 Search in Google Scholar

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 Search in Google Scholar

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 Search in Google Scholar

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 Search in Google Scholar

Nielsen R (2005) Molecular signatures of natural selection. Annu Rev Genet. 39, 197-218. https://doi.org/10.1146/annurev.genet.39.073003.112420 Search in Google Scholar

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 Search in Google Scholar

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 Search in Google Scholar

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 Search in Google Scholar