| [1] Margulies M, Egholm M, Altman WE, Attiya S, Bader JS, Bemben LA, Berka J, Braverman MS, Chen YJ, Chen Z, Dewell SB, Du L, Fierro JM, Gomes XV, Godwin BC, He W, Helgesen S, Ho CH, Irzyk GP, Jando SC, Alenquer ML, Jarvie TP, Jirage KB, Kim JB, Knight JR, Lanza JR, Leamon JH, Lefkowitz SM, Lei M, Li J, Lohman KL, Lu H, Makhijani VB, McDade KE, McKenna MP, Myers EW, Nickerson E, Nobile JR, Plant R, Puc BP, Ronan MT, Roth GT, Sarkis GJ, Simons JF, Simpson JW, Srinivasan M, Tartaro KR, Tomasz A, Vogt KA, Volkmer GA, Wang SH, Wang Y, Weiner MP, Yu P, Begley RF, Rothberg JM. Genome sequencing in microfabricated high-density picolitre reactors. Nature, 2005, 437(7057): 376–380. <\p>
[2] Altshuler D, Pollara VJ, Cowles CR, van Etten WJ, Baldwin J, Linton L, Lander ES. An SNP map of the human genome generated by reduced representation shotgun sequencing. Nature, 2000, 407(6803): 513–516. <\p>
[3] Davey JL, Blaxter MW. RADSeq: next-generation popu-lation genetics. Brief Funct Genomic, 2010, 9(5?6): 416– 423. <\p>
[4] Elshire RJ, Glaubitz JC, Sun Q, Poland JA, Kawamoto K, Buckler ES, Mitchell SE. A robust, simple genotyping- by-sequencing (GBS) approach for high diversity species. PloS ONE, 2011, 6(5): e19379. <\p>
[5] Miller MR, Dunham JP, Amores A, Cresko WA, Johnson EA. Rapid and cost-effective polymorphism identification and genotyping using restriction site associated DNA (RAD) markers. Genome Res, 2007, 17(2): 240–248. <\p>
[6] van Tassell CP, Smith TP, Matukumalli LK, Taylor JF, Schnabel RD, Lawley CT, Haudenschild CD, Moore SS, Warren WC, Sonstegard TS. SNP discovery and allele frequency estimation by deep sequencing of reduced re-presentation libraries. Nat Methods, 2008, 5(3): 247–252. <\p>
[7] Emerson KJ, Merz CR, Catchen JM, Hohenlohe PA, Cresko WA, Bradshaw WE, Holzapfel CM. Resolving postglacial phylogeography using high-throughput sequencing. Proc Natl Acad Sci USA, 2010, 107(37): 16196– 16200. <\p>
[8] Hohenlohe PA, Amish JS, Catchen MJ, Allendorf WF, Luikart G. Next-generation RAD sequencing identifies thousands of SNPs for assessing hybridization between rainbow and westslope cutthroat trout. Mol Ecol Resour, 2011, 11(Suppl. 1): 117–122. <\p>
[9] Pfender WF, Saha MC, Johnson EA, Slabaugh MB. Mapping with RAD (restriction-site associated DNA) markers to rapidly identify QTL for stem rust resistance in Lolium perenne. Theor Appl Genet, 2011, 122(8): 1467–1480. <\p>
[10] Poland JA, Brown PJ, Sorrells ME, Jannink JL. Develop-ment of high-density genetic maps for barley and wheat using a novel two-enzyme genotyping-by-sequencing ap-proach. PloS ONE, 2012, 7(2): e32253. <\p>
[11] Baird NA, Etter PD, Atwood TS, Currey MC, Shiver AL, Lewis ZA, Johnson EA. Rapid SNP discovery and genetic mapping using sequenced RAD markers. PLoS ONE, 2008, 3(10): e3376. <\p>
[12] Catchen JM, Amores A, Hohenlohe P, Cresko W, Post-lethwait JH. Stacks: building and genotyping Loci de novo from short-read sequences. G3, 2011, 1(3): 171–182. <\p>
[13] Catchen JM, Hohenlohe P, Bassham S, Amores A, Cresko WA. Stacks: an analysis tool set for population genomics. Mol Ecol, 2013, 22(11): 3124–3140. <\p>
[14] Edgar RC. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res, 2004, 32(5): 1792–1797. <\p>
[15] Altschul SF, Madden TL, Schäffer AA, Zhang JH, Zhang Z, Miller W, Lipman DJ. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res, 1997, 25(17): 3389–3402. <\p>
[16] Kent WJ. BLAT-the BLAST-like alignment tool. Genome Res, 2002, 12(4): 656–664. <\p>
[17] Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Durbin R. The sequence alignment/map format and SAM |
