PAV markers in Sorghum bicolour: genome pattern, affected genes and pathways, and genetic linkage map construction

Theoretical and Applied Genetics

Volumn 128, Issue 4, 2015, Pages 623-637

  Shen, Xin ^a,c   Liu, Zhi Quan ^a   Mocoeur, Anne ^a,b   Xia, Yan ^a   Jing, Hai Chun ^a  

^a INSTITUTE OF GEOLOGY AND GEOPHYSICS   (China)

^b UNIVERSITY OF COPENHAGEN   (Denmark)

^c UNIVERSITY OF CHINESE ACADEMY OF SCIENCES   (China)

Author keywords

[No Author keywords available]

Indexed keywords

PLANTS (BOTANY);

CENTROMERIC REGIONS; CODING SEQUENCES; GENOME SEQUENCING; LONG TERMINAL REPEATS; PHENOTYPIC VARIATIONS; PRESENCE/ABSENCE; PROMINENT FEATURES; PROTEIN MODIFICATIONS;

GENES;

MICROSATELLITE DNA; PLANT DNA; RETROPOSON;

BREEDING; CENTROMERE; CHROMOSOMAL MAPPING; DNA SEQUENCE; GENETIC LINKAGE; GENETICS; GENOME SIZE; PLANT GENOME; RETROPOSON; SORGHUM;

BREEDING; CENTROMERE; CHROMOSOME MAPPING; DNA, PLANT; GENETIC LINKAGE; GENOME SIZE; GENOME, PLANT; MICROSATELLITE REPEATS; RETROELEMENTS; SEQUENCE ANALYSIS, DNA; SORGHUM;

EID: 84925517699     PISSN: 00405752     EISSN: 14322242     Source Type: Journal    
DOI: 10.1007/s00122-015-2458-4     Document Type: Article

References (94)

1. Andersen JR, Lübberstedt T (2003) Functional markers in plants. Trends Plant Sci 8(11):554–560. doi:10.1016/j.tplants.2003.09.010
2. Arrach N, Porwollik S, Cheng P, Cho A, Long F, Choi SH, McClelland M (2008) Salmonella serovar identification using PCR-based detection of gene presence and absence. J Clin Microbiol 46(8):2581–2589. doi:10.1128/Jcm.02147-07
3. Barnaud A, Trigueros G, Mckey D, Joly HI (2008) High outcrossing rates in fields with mixed sorghum landraces: how are landraces maintained? Heredity 101(5):445–452. doi:10.1038/Hdy.2008.77
4. Bekele WA, Wieckhorst S, Friedt W, Snowdon RJ (2013) High-throughput genomics in sorghum: from whole-genome resequencing to a SNP screening array. Plant Biotechnol J 11(9):1112–1125. doi:10.1111/Pbi.12106
5. Bennetzen JL (2000) Transposable element contributions to plant gene and genome evolution. Plant Mol Biol 42(1):251–269. doi:10.1023/A:1006344508454
6. Bhattramakki D, Dong JM, Chhabra AK, Hart GE (2000) An integrated SSR and RFLP linkage map of Sorghum bicolour (L.) Moench. Genome/National Research Council Canada = Genome/Conseil national de recherches Canada 43(6):988–1002. doi:10.1139/Gen-43-6-988
7. Boivin K, Deu M, Rami JF, Trouche G, Hamon P (1999) Towards a saturated sorghum map using RFLP and AFLP markers. Theor Appl Genet 98(2):320–328. doi:10.1007/s001220051076
8. Bouchet S, Pot D, Deu M, Rami JF, Billot C, Perrier X, Rivallan R, Gardes L, Xia L, Wenzl P, Kilian A, Glaszmann JC (2012) Genetic structure, linkage disequilibrium and signature of selection in sorghum: lessons from physically anchored DArT markers. PloS One 7(3). doi:10.1371/journal.pone.0033470
9. Bowers JE, Abbey C, Anderson S, Chang C, Draye X, Hoppe AH, Jessup R, Lemke C, Lennington J, Li ZK, Lin YR, Liu SC, Luo LJ, Marler BS, Ming RG, Mitchell SE, Qiang D, Reischmann K, Schulze SR, Skinner DN, Wang YW, Kresovich S, Schertz KF, Paterson AH (2003) A high-density genetic recombination map of sequence-tagged sites for sorghum, as a framework for comparative structural and evolutionary genomics of tropical grains and grasses. Genetics 165(1):367–386
10. Bush SJ, Castillo-Morales A, Tovar-Corona JM, Chen L, Kover PX, Urrutia AO (2014) Presence–absence variation in A. thaliana is primarily associated with genomic signatures consistent with relaxed selective constraints. Mol Biol Evol 31(1):59–69. doi:10.1093/molbev/mst166
11. Cheema J, Dicks J (2009) Computational approaches and software tools for genetic linkage map estimation in plants. Brief Bioinform 10(6):595–608. doi:10.1093/Bib/Bbp045
12. Conrad DF, Pinto D, Redon R, Feuk L, Gokcumen O, Zhang YJ, Aerts J, Andrews TD, Barnes C, Campbell P, Fitzgerald T, Hu M, Ihm CH, Kristiansson K, MacArthur DG, MacDonald JR, Onyiah I, Pang AWC, Robson S, Stirrups K, Valsesia A, Walter K, Wei J, Tyler-Smith C, Carter NP, Lee C, Scherer SW, Hurles ME, Control WTC (2010) Origins and functional impact of copy number variation in the human genome. Nature 464(7289):704–712. doi:10.1038/Nature08516
13. Dahlberg JA, Zhang X, Hart GE, Mullet JE (2002) Comparative assessment of variation among sorghum germplasm accessions using seed morphology and RAPD measurements. Crop Sci 42(1):291–296
14. Dalal M, Mayandi K, Chinnusamy V (2012) Sorghum: improvement of abiotic stress tolerance. In: Improving crop resistance to abiotic stress. Wiley-VCH Verlag GmbH & Co. KGaA, pp 923–950. doi:10.1002/9783527632930.ch36
15. Ding J, Araki H, Wang Q, Zhang P, Yang S, Chen JQ, Tian D (2007) Highly asymmetric rice genomes. BMC Genomics 8. doi:10.1186/1471-2164-8-154
16. Doyle JJ (1987) A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochem Bull 19:11–15
17. Du Z, Zhou X, Ling Y, Zhang ZH, Su Z (2010) agriGO: a GO analysis toolkit for the agricultural community. Nucleic Acids Res 38:W64–W70. doi:10.1093/Nar/Gkq310
18. Dufour P, Deu M, Grivet L, D'Hont A, Paulet F, Bouet A, Lanaud C, Glaszmann JC, Hamon P (1997) Construction of a composite sorghum genome map and comparison with sugarcane, a related complex polyploid. Theor Appl Genet 94(3–4):409–418. doi:10.1007/s001220050430
19. FAO (2004) Food and Agriculture Organization of the United Nations, Statistics Division. http://www.fao.org/es/ess/index_en.asp
20. Felcher KJ, Coombs JJ, Massa AN, Hansey CN, Hamilton JP, Veilleux RE, Buell CR, Douches DS (2012) Integration of two diploid potato linkage maps with the potato genome sequence. PloS One 7(4). doi:10.1371/journal.pone.0036347
21. Felderhoff TJ, Murray SC, Klein PE, Sharma A, Hamblin MT, Kresovich S, Vermerris W, Rooney WL (2012) QTLs for energy-related traits in a sweet x grain sorghum [Sorghum bicolor (L.) Moench] mapping population. Crop Sci 52(5):2040–2049. doi:10.2135/cropsci2011.11.0618
22. Feuk L, Carson AR, Scherer SW (2006) Structural variation in the human genome. Nat Rev Genet 7(2):85–97. doi:10.1038/Nrg1767
23. Gan XC, Stegle O, Behr J, Steffen JG, Drewe P, Hildebrand KL, Lyngsoe R, Schultheiss SJ, Osborne EJ, Sreedharan VT, Kahles A, Bohnert R, Jean G, Derwent P, Kersey P, Belfield EJ, Harberd NP, Kemen E, Toomajian C, Kover PX, Clark RM, Ratsch G, Mott R (2011) Multiple reference genomes and transcriptomes for Arabidopsis thaliana. Nature 477(7365):419–423. doi:10.1038/Nature10414
24. Ganal MW, Durstewitz G, Polley A, Berard A, Buckler ES, Charcosset A, Clarke JD, Graner EM, Hansen M, Joets J, Le Paslier MC, McMullen MD, Montalent P, Rose M, Schon CC, Sun Q, Walter H, Martin OC, Falque M (2011) A large maize (Zea mays L.) SNP genotyping array: development and germplasm genotyping, and genetic mapping to compare with the B73 reference genome. PloS One 6(12). doi:10.1371/journal.pone.0028334
25. Gonzalez VM, Aventin N, Centeno E, Puigdomenech P (2013) High presence/absence gene variability in defense-related gene clusters of Cucumis melo. BMC Genomics 14. doi:10.1186/1471-2164-14-782
26. Grant MR, McDowell JM, Sharpe AG, Zabala MDT, Lydiate DJ, Dangl JL (1998) Independent deletions of a pathogen-resistance gene in Brassica and Arabidopsis. Proc Natl Acad Sci USA 95(26):15843–15848. doi:10.1073/pnas.95.26.15843
27. Hamblin MT, Mitchell SE, White GM, Gallego W, Kukatla R, Wing RA, Paterson AH, Kresovich S (2004) Comparative population genetics of the panicoid grasses: sequence polymorphism, linkage disequilibrium and selection in a diverse sample of Sorghum bicolour. Genetics 167(1):471–483. doi:10.1534/genetics.167.1.471
28. Hastings PJ, Lupski JR, Rosenberg SM, Ira G (2009) Mechanisms of change in gene copy number. Nat Rev Genet 10(8):551–564. doi:10.1038/Nrg2593
29. Hulbert SH, Richter TE, Axtell JD, Bennetzen JL (1990) Genetic mapping and characterization of sorghum and related crops by means of maize DNA probes. Proc Natl Acad Sci USA 87(11):4251–4255
30. Iafrate AJ, Feuk T, Van Puymbroeck L, Rivera MN, Listewnik ML, Ying QP, Scherer SW, Lee C (2004) Detection of large-scale variation in the human genome. J Mol Diagn 6(4):411
31. Kebede H, Subudhi PK, Rosenow DT, Nguyen HT (2001) Quantitative trait loci influencing drought tolerance in grain sorghum (Sorghum bicolour L. Moench). Theor Appl Genet 103(2–3):266–276. doi:10.1007/s001220100541
32. Kern AD, Begun DJ (2008) Current deletion and gene presence/absence polymorphism: telomere dynamics dominate evolution at the tip of 3L in Drosophila melanogaster and D-simulans. Genetics 179(2):1021–1027. doi:10.1534/genetics.107.078345
33. Kidd JM, Cooper GM, Donahue WF, Hayden HS, Sampas N, Graves T, Hansen N, Teague B, Alkan C, Antonacci F, Haugen E, Zerr T, Yamada NA, Tsang P, Newman TL, Tuzun E, Cheng Z, Ebling HM, Tusneem N, David R, Gillett W, Phelps KA, Weaver M, Saranga D, Brand A, Tao W, Gustafson E, McKernan K, Chen L, Malig M, Smith JD, Korn JM, McCarroll SA, Altshuler DA, Peiffer DA, Dorschner M, Stamatoyannopoulos J, Schwartz D, Nickerson DA, Mullikin JC, Wilson RK, Bruhn L, Olson MV, Kaul R, Smith DR, Eichler EE (2008) Mapping and sequencing of structural variation from eight human genomes. Nature 453(7191):56–64. doi:10.1038/Nature06862
34. Kidwell MG, Lisch D (1997) Transposable elements as sources of variation in animals and plants. Proc Natl Acad Sci USA 94(15):7704–7711. doi:10.1073/pnas.94.15.7704
35. Kim JS, Islam-Faridi MN, Klein PE, Stelly DM, Price HJ, Klein RR, Mullet JE (2005) Comprehensive molecular cytogenetic analysis of sorghum genome architecture: distribution of euchromatin, heterochromatin, genes and recombination in comparison to rice. Genetics 171(4):1963–1976. doi:10.1534/genetics.105.048215
36. Kolliker R, Jones ES, Drayton MC, Dupal MP, Forster JW (2001) Development and characterisation of simple sequence repeat (SSR) markers for white clover (Trifolium repens L.). Theor Appl Genet 102(2–3):416–424. doi:10.1007/s001220051662
37. Kong L, Dong J, Hart GE (2000) Characteristics, linkage-map positions, and allelic differentiation of Sorghum bicolour (L.) Moench DNA simple-sequence repeats (SSRs). Theor Appl Genet 101(3):438–448. doi:10.1007/s001220051501
38. Korbel JO, Urban AE, Affourtit JP, Godwin B, Grubert F, Simons JF, Kim PM, Palejev D, Carriero NJ, Du L, Taillon BE, Chen ZT, Tanzer A, Saunders ACE, Chi JX, Yang FT, Carter NP, Hurles ME, Weissman SM, Harkins TT, Gerstein MB, Egholm M, Snyder M (2007) Paired-end mapping reveals extensive structural variation in the human genome. Science 318(5849):420–426. doi:10.1126/science.1149504
39. Kosambi DD (1943) The estimation of map distances from recombination values. Ann Eugen 12:172–175
40. Lam HM, Xu X, Liu X, Chen WB, Yang GH, Wong FL, Li MW, He WM, Qin N, Wang B, Li J, Jian M, Wang JA, Shao GH, Wang J, Sun SSM, Zhang GY (2010) Resequencing of 31 wild and cultivated soybean genomes identifies patterns of genetic diversity and selection. Nat Genet 42(12):1053–1059. doi:10.1038/Ng.715
41. Lee HR, Zhang WL, Langdon T, Jin WW, Yan HH, Cheng ZK, Jiang JM (2005) Chromatin immunoprecipitation cloning reveals rapid evolutionary patterns of centromeric DNA in Oryza species. Proc Natl Acad Sci USA 102(33):11793–11798. doi:10.1073/pnas.0503863102
42. Li RQ, Yu C, Li YR, Lam TW, Yiu SM, Kristiansen K, Wang J (2009) SOAP2: an improved ultrafast tool for short read alignment. Bioinformatics 25(15):1966–1967. doi:10.1093/bioinformatics/btp336
43. Mace ES, Jordan DR (2011) Integrating sorghum whole genome sequence information with a compendium of sorghum QTL studies reveals uneven distribution of QTL and of gene-rich regions with significant implications for crop improvement. Theor Appl Genet 123(1):169–191. doi:10.1007/s00122-011-1575-y
44. Mace ES, Xia L, Jordan DR, Halloran K, Parh DK, Huttner E, Wenzl P, Kilian A (2008) DArT markers: diversity analyses and mapping in Sorghum bicolour. BMC Genomics 9. doi:10.1186/1471-2164-9-26
45. Mace ES, Rami JF, Bouchet S, Klein PE, Klein RR, Kilian A, Wenzl P, Xia L, Halloran K, Jordan DR (2009) A consensus genetic map of sorghum that integrates multiple component maps and high-throughput Diversity Array Technology (DArT) markers. BMC Plant Biol 9. doi:10.1186/1471-2229-9-13
46. Mace ES, Tai S, Gilding EK, Li Y, Prentis PJ, Bian L, Campbell BC, Hu W, Innes DJ, Han X, Cruickshank A, Dai C, Frere C, Zhang H, Hunt CH, Wang X, Shatte T, Wang M, Su Z, Li J, Lin X, Godwin ID, Jordan DR, Wang J (2013) Whole-genome sequencing reveals untapped genetic potential in Africa’s indigenous cereal crop sorghum. Nat Commun 4:2320. doi:10.1038/ncomms3320
47. Marroni F, Pinosio S, Morgante M (2014) Structural variation and genome complexity: is dispensable really dispensable? Curr Opin Plant Biol 18:31–36. doi:10.1016/j.pbi.2014.01.003
48. Mcclintock B (1948) Mutable loci in maize. Carnegie Inst Wash 47:155–169
49. McCouch SR, Chen XL, Panaud O, Temnykh S, Xu YB, Cho YG, Huang N, Ishii T, Blair M (1997) Microsatellite marker development, mapping and applications in rice genetics and breeding. Plant Mol Biol 35(1–2):89–99. doi:10.1023/A:1005711431474
50. McHale LK, Haun WJ, Xu WW, Bhaskar PB, Anderson JE, Hyten DL, Gerhardt DJ, Jeddeloh JA, Stupar RM (2012) Structural variants in the soybean genome localize to clusters of biotic stress-response genes. Plant Physiol 159(4):1295–1308. doi:10.1104/pp.112.194605
51. McKernan KJ, Peckham HE, Costa GL, McLaughlin SF, Fu YT, Tsung EF, Clouser CR, Duncan C, Ichikawa JK, Lee CC, Zhang Z, Ranade SS, Dimalanta ET, Hyland FC, Sokolsky TD, Zhang L, Sheridan A, Fu HN, Hendrickson CL, Li B, Kotler L, Stuart JR, Malek JA, Manning JM, Antipova AA, Perez DS, Moore MP, Hayashibara KC, Lyons MR, Beaudoin RE, Coleman BE, Laptewicz MW, Sannicandro AE, Rhodes MD, Gottimukkala RK, Yang S, Bafna V, Bashir A, MacBride A, Alkan C, Kidd JM, Eichler EE, Reese MG, De la Vega FM, Blanchard AP (2009) Sequence and structural variation in a human genome uncovered by short-read, massively parallel ligation sequencing using two-base encoding. Genome Res 19(9):1527–1541. doi:10.1101/gr.091868.109
52. Menz MA, Klein RR, Mullet JE, Obert JA, Unruh NC, Klein PE (2002) A high-density genetic map of Sorghum bicolour (L.) Moench based on 2926 AFLP (R), RFLP and SSR markers. Plant Mol Biol 48(5):483–499. doi:10.1023/A:1014831302392
53. Menz MA, Klein RR, Unruh NC, Rooney WL, Klein PE, Mullet JE (2004) Genetic diversity of public inbreds of sorghum determined by mapped AFLP and SSR markers. Crop Sci 44:1236–1244
54. Miller JT, Jackson SA, Nasuda S, Gill BS, Wing RA, Jiang J (1998) Cloning and characterization of a centromere-specific repetitive DNA element from Sorghum bicolour. Theor Appl Genet 96(6–7):832–839. doi:10.1007/s001220050809
55. Mills RE, Walter K, Stewart C, Handsaker RE, Chen K, Alkan C, Abyzov A, Yoon SC, Ye K, Cheetham RK, Chinwalla A, Conrad DF, Fu YT, Grubert F, Hajirasouliha I, Hormozdiari F, Iakoucheva LM, Iqbal Z, Kang SL, Kidd JM, Konkel MK, Korn J, Khurana E, Kural D, Lam HYK, Leng J, Li RQ, Li YR, Lin CY, Luo RB, Mu XJ, Nemesh J, Peckham HE, Rausch T, Scally A, Shi XH, Stromberg MP, Stutz AM, Urban AE, Walker JA, Wu JT, Zhang YJ, Zhang ZDD, Batzer MA, Ding L, Marth GT, McVean G, Sebat J, Snyder M, Wang J, Ye K, Eichler EE, Gerstein MB, Hurles ME, Lee C, McCarroll SA, Korbel JO, Project G (2011) Mapping copy number variation by population-scale genome sequencing. Nature 470(7332):59–65. doi:10.1038/Nature09708
56. Morgante M, Brunner S, Pea G, Fengler K, Zuccolo A, Rafalski A (2005) Gene duplication and exon shuffling by helitron-like transposons generate intraspecies diversity in maize. Nat Genet 37(9):997–1002. doi:10.1038/Ng1615
57. Murphy WJ, Larkin DM, Everts-van der Wind A, Bourque G, Tesler G, Auvil L, Beever JE, Chowdhary BP, Galibert F, Gatzke L, Hitte C, Meyers SN, Milan D, Ostrander EA, Pape G, Parker HG, Raudsepp T, Rogatcheva MB, Schook LB, Skow LC, Welge M, Womack JE, O’Brien SJ, Pevzner PA, Lewin HA (2005) Dynamics of mammalian chromosome evolution inferred from multispecies comparative maps. Science 309(5734):613–617. doi:10.1126/science.1111387
58. Murray SC, Sharma A, Rooney WL, Klein PE, Mullet JE, Mitchell SE, Kresovich S (2008) Genetic improvement of sorghum as a biofuel feedstock: I. QTL for stem sugar and grain nonstructural carbohydrates. Crop Sci 48(6):2165–2179. doi:10.2135/cropsci2008.01.0016
59. Paterson AH, Bowers JE, Bruggmann R, Dubchak I, Grimwood J, Gundlach H, Haberer G, Hellsten U, Mitros T, Poliakov A, Schmutz J, Spannagl M, Tang H, Wang X, Wicker T, Bharti AK, Chapman J, Feltus FA, Gowik U, Grigoriev IV, Lyons E, Maher CA, Martis M, Narechania A, Otillar RP, Penning BW, Salamov AA, Wang Y, Zhang L, Carpita NC, Freeling M, Gingle AR, Hash CT, Keller B, Klein P, Kresovich S, McCann MC, Ming R, Peterson DG, Mehboob ur R, Ware D, Westhoff P, Mayer KF, Messing J, Rokhsar DS (2009) The Sorghum bicolour genome and the diversification of grasses. Nature 457(7229):551–556. doi:10.1038/nature07723
60. Punta M, Coggill PC, Eberhardt RY, Mistry J, Tate J, Boursnell C, Pang N, Forslund K, Ceric G, Clements J, Heger A, Holm L, Sonnhammer ELL, Eddy SR, Bateman A, Finn RD (2012) The Pfam protein families database. Nucleic Acids Res 40(D1):D290–D301. doi:10.1093/Nar/Gkr1065
61. Qi X, Pittaway TS, Lindup S, Liu H, Waterman E, Padi FK, Hash CT, Zhu J, Gale MD, Devos KM (2004) An integrated genetic map and a new set of simple sequence repeat markers for pearl millet, Pennisetum glaucum. Theor Appl Genet 109(7):1485–1493. doi:10.1007/s00122-004-1765-y
62. Redon R, Ishikawa S, Fitch KR, Feuk L, Perry GH, Andrews TD, Fiegler H, Shapero MH, Carson AR, Chen WW, Cho EK, Dallaire S, Freeman JL, Gonzalez JR, Gratacos M, Huang J, Kalaitzopoulos D, Komura D, MacDonald JR, Marshall CR, Mei R, Montgomery L, Nishimura K, Okamura K, Shen F, Somerville MJ, Tchinda J, Valsesia A, Woodwark C, Yang FT, Zhang JJ, Zerjal T, Zhang J, Armengol L, Conrad DF, Estivill X, Tyler-Smith C, Carter NP, Aburatani H, Lee C, Jones KW, Scherer SW, Hurles ME (2006) Global variation in copy number in the human genome. Nature 444(7118):444–454. doi:10.1038/Nature05329
63. Sebat J, Lakshmi B, Malhotra D, Troge J, Lese-Martin C, Walsh T, Yamrom B, Yoon S, Krasnitz A, Kendall J, Leotta A, Pai D, Zhang R, Lee YH, Hicks J, Spence SJ, Lee AT, Puura K, Lehtimaki T, Ledbetter D, Gregersen PK, Bregman J, Sutcliffe JS, Jobanputra V, Chung W, Warburton D, King MC, Skuse D, Geschwind DH, Gilliam TC, Ye K, Wigler M (2007) Strong association of de novo copy number mutations with autism. Science 316(5823):445–449. doi:10.1126/science.1138659
64. Shen JD, Araki H, Chen LL, Chen JQ, Tian DC (2006) Unique evolutionary mechanism in R-genes under the presence/absence polymorphism in Arabidopsis thaliana. Genetics 172(2):1243–1250. doi:10.1534/genetics.105.047290
65. Shi JH, Wolf SE, Burke JM, Presting GG, Ross-Ibarra J, Dawe RK (2010) Widespread gene conversion in centromere cores. Plos Biol 8(3). doi:10.1371/journal.pbio.1000327
66. Sim SC, Durstewitz G, Plieske J, Wieseke R, Ganal MW, Van Deynze A, Hamilton JP, Buell CR, Causse M, Wijeratne S, Francis DM (2012) Development of a large SNP genotyping array and generation of high-density genetic maps in tomato. PloS One 7(7). doi:10.1371/journal.pone.0040563
67. Smedley D, Haider S, Ballester B, Holland R, London D, Thorisson G, Kasprzyk A (2009) BioMart—biological queries made easy. BMC Genomics 10. doi:10.1186/1471-2164-10-22
68. Springer NM, Ying K, Fu Y, Ji TM, Yeh CT, Jia Y, Wu W, Richmond T, Kitzman J, Rosenbaum H, Iniguez AL, Barbazuk WB, Jeddeloh JA, Nettleton D, Schnable PS (2009) Maize inbreds exhibit high levels of copy number variation (CNV) and presence/absence variation (PAV) in genome content. Plos Genet 5(11). doi:10.1371/journal.pgen.1000734
69. Stefansson H, Helgason A, Thorleifsson G, Steinthorsdottir V, Masson G, Barnard J, Baker A, Jonasdottir A, Ingason A, Gudnadottir VG, Desnica N, Hicks A, Gylfason A, Gudbjartsson DF, Jonsdottir GM, Sainz J, Agnarsson K, Birgisdottir B, Ghosh S, Olafsdottir A, Cazier JB, Kristjansson K, Frigge ML, Thorgeirsson TE, Gulcher JR, Kong A, Stefansson K (2005) A common inversion under selection in Europeans. Nat Genet 37(2):129–137. doi:10.1038/Ng1508
70. Subudhi PK, Nguyen HT (2000) Linkage group alignment of sorghum RFLP maps using a RIL mapping population. Genome/National Research Council Canada = Genome/Conseil national de recherches Canada 43(2):240–249. doi:10.1139/Gen-43-2-240
71. Swanson-Wagner RA, Eichten SR, Kumari S, Tiffin P, Stein JC, Ware D, Springer NM (2010) Pervasive gene content variation and copy number variation in maize and its undomesticated progenitor. Genome Res 20(12):1689–1699. doi:10.1101/gr.109165.110
72. Tan SJ, Zhong Y, Hou H, Yang SH, Tian DC (2012) Variation of presence/absence genes among Arabidopsis populations. BMC Evol Biol 12. doi:10.1186/1471-2148-12-86
73. Tenaillon MI, Hollister JD, Gaut BS (2010) A triptych of the evolution of plant transposable elements. Trends Plant Sci 15(8):471–478. doi:10.1016/j.tplants.2010.05.003
74. Tuzun E, Sharp AJ, Bailey JA, Kaul R, Morrison VA, Pertz LM, Haugen E, Hayden H, Albertson D, Pinkel D, Olson MV, Eichler EE (2005) Fine-scale structural variation of the human genome. Nat Genet 37(7):727–732. doi:10.1038/Ng1562
75. Van Berloo R (2008) GGT 2.0: versatile software for visualization and analysis of genetic data. J Hered 99(2):232–236. doi:10.1093/jhered/esm109
76. Van Os H, Andrzejewski S, Bakker E, Barrena I, Bryan GJ, Caromel B, Ghareeb B, Isidore E, de Jong W, van Koert P, Lefebvre V, Milbourne D, Ritter E, van der Voort JNAMR, Rousselle-Bourgeois F, van Vliet J, Waugh R, Visser RGF, Bakker J, van Eck HJ (2006) Construction of a 10,000-marker ultradense genetic recombination map of potato: providing a framework for accelerated gene isolation and a genomewide physical map. Genetics 173(2):1075–1087. doi:10.1534/genetics.106.055871
77. Vos P, Hogers R, Bleeker M, Reijans M, Vandelee T, Hornes M, Frijters A, Pot J, Peleman J, Kuiper M, Zabeau M (1995) Aflp—a new technique for DNA-fingerprinting. Nucleic Acids Res 23(21):4407–4414. doi:10.1093/nar/23.21.4407
78. Wang X, Weigel D, Smith LM (2013) Transposon variants and their effects on gene expression in Arabidopsis. Plos Genet 9(2). doi:10.1371/journal.pgen.1003255
79. Wang Y, Lu J, Chen S, Shu L, Palmer RG, Xing G, Li Y, Yang S, Yu D, Zhao T (2014) Exploration of presence/absence variation and corresponding polymorphic markers in soybean genome. J Integr Plant Biol 56:1009–1019
80. Whitkus R, Doebley J, Lee M (1992) Comparative genome mapping of sorghum and maize. Genetics 132(4):1119–1130
81. Wu YQ, Huang YH (2007) An SSR genetic map of Sorghum bicolour (L.) Moench and its comparison to a published genetic map. Genome/National Research Council Canada = Genome/Conseil national de recherches Canada 50(1):84–89. doi:10.1139/G06-133
82. Wu DH, Wu HP, Wang CS, Tseng HY, Hwu KK (2013) Genome-wide InDel marker system for application in rice breeding and mapping studies. Euphytica 192(1):131–143. doi:10.1007/s10681-013-0925-z
83. Xu GW, Magill CW, Schertz KF, Hart GE (1994) A RFLP linkage map of Sorghumbicolour (L) Moench. Theor Appl Genet 89(2–3):139–145
84. Yalcin B, Wong K, Agam A, Goodson M, Keane TM, Gan XC, Nellaker C, Goodstadt L, Nicod J, Bhomra A, Hernandez-Pliego P, Whitley H, Cleak J, Dutton R, Janowitz D, Mott R, Adams DJ, Flint J (2011) Sequence-based characterization of structural variation in the mouse genome. Nature 477(7364):326–329. doi:10.1038/Nature10432
85. Ye J, Fang L, Zheng HK, Zhang Y, Chen J, Zhang ZJ, Wang J, Li ST, Li RQ, Bolund L, Wang J (2006) WEGO: a web tool for plotting GO annotations. Nucleic Acids Res 34:W293–W297. doi:10.1093/Nar/Gkl1031
86. Yu J, Wang J, Lin W, Li SG, Li H, Zhou J, Ni PX, Dong W, Hu SN, Zeng CQ, Zhang JG, Zhang Y, Li RQ, Xu ZY, Li ST, Li XR, Zheng HK, Cong LJ, Lin L, Yin JN, Geng JN, Li GY, Shi JP, Liu J, Lv H, Li J, Wang J, Deng YJ, Ran LH, Shi XL, Wang XY, Wu QF, Li CF, Ren XY, Wang JQ, Wang XL, Li DW, Liu DY, Zhang XW, Ji ZD, Zhao WM, Sun YQ, Zhang ZP, Bao JY, Han YJ, Dong LL, Ji J, Chen P, Wu SM, Liu JS, Xiao Y, Bu DB, Tan JL, Yang L, Ye C, Zhang JF, Xu JY, Zhou Y, Yu YP, Zhang B, Zhuang SL, Wei HB, Liu B, Lei M, Yu H, Li YZ, Xu H, Wei SL, He XM, Fang LJ, Zhang ZJ, Zhang YZ, Huang XG, Su ZX, Tong W, Li JH, Tong ZZ, Li SL, Ye J, Wang LS, Fang L, Lei TT, Chen C, Chen H, Xu Z, Li HH, Huang HY, Zhang F, Xu HY, Li N, Zhao CF, Li ST, Dong LJ, Huang YQ, Li L, Xi Y, Qi QH, Li WJ, Zhang B, Hu W, Zhang YL, Tian XJ, Jiao YZ, Liang XH, Jin JA, Gao L, Zheng WM, Hao BL, Liu SQ, Wang W, Yuan LP, Cao ML, McDermott J, Samudrala R, Wang J, Wong GKS, Yang HM (2005) The genomes of Oryza sativa: a history of duplications. PLoS Biol 3(2):266–281. doi:10.1371/journal.pbio.0030038
87. Yu C-Z, Zhai G-W, Zou G-H, Y-z TAO, Wang H (2010) Assessment of genetic diversity among 41 sorghum varieties using SSR markers. Jiangsu J Agric Sci 2:007
88. Zhang F, Gu WL, Hurles ME, Lupski JR (2009) Copy number variation in human health, disease, and evolution. Annu Rev Genomics Hum Genet 10:451–481. doi:10.1146/annurev.genom.9.081307.164217
89. Zhang WW, Pan JS, He HL, Zhang C, Li Z, Zhao JL, Yuan XJ, Zhu LH, Huang SW, Cai R (2012) Construction of a high density integrated genetic map for cucumber (Cucumis sativus L.). Theor Appl Genet 124(2):249–259. doi:10.1007/s00122-011-1701-x
90. Zhang LM, Luo H, Liu ZQ, Zhao Y, Luo JC, Hao DY, Jing HC (2014) Genome-wide patterns of large-size presence/absence variants in sorghum. J Integr Plant Biol 56(1):24–37. doi:10.1111/Jipb.12121
91. Zheng LY, Guo XS, He B, Sun LJ, Peng Y, Dong SS, Liu TF, Jiang SY, Ramachandran S, Liu CM, Jing HC (2011) Genome-wide patterns of genetic variation in sweet and grain sorghum (Sorghum bicolour). Genome Biol 12(11). doi:10.1186/Gb-2011-12-11-R114
92. Ziolkowski PA, Koczyk G, Galganski L, Sadowski J (2009) Genome sequence comparison of Col and Ler lines reveals the dynamic nature of Arabidopsis chromosomes. Nucleic Acids Res 37(10):3189–3201. doi:10.1093/Nar/Gkp183
93. Zou GH, Zhai GW, Feng Q, Yan S, Wang A, Zhao Q, Shao JF, Zhang ZP, Zou JQ, Han B, Tao YZ (2012) Identification of QTLs for eight agronomically important traits using an ultra-high-density map based on SNPs generated from high-throughput sequencing in sorghum under contrasting photoperiods. J Exp Bot 63(15):5451–5462
94. Zwick MS, Islam-Faridi MN, Zhang HB, Hodnett GL, Gomez MI, Kim JS, Price HJ, Stelly DM (2000) Distribution and sequence analysis of the centromere-associated repetitive element CEN38 of Sorghum bicolour (Poaceae). Am J Bot 87(12):1757–1764. doi:10.2307/2656825