Genome-wide patterns of large-size presence/absence variants in sorghum

Journal of Integrative Plant Biology

Volumn 56, Issue 1, 2014, Pages 24-37

  Zhang, Li Min ^a,b   Luo, Hong ^a   Liu, Zhi Quan ^a   Zhao, Yi ^c   Luo, Jing Chu ^c   Hao, Dong Yun ^b,d   Jing, Hai Chun ^a  

^a INSTITUTE OF BOTANY   (China)

^b JILIN UNIVERSITY   (China)

^c PEKING UNIVERSITY   (China)

^d JILIN ACADEMY OF AGRICULTURAL SCIENCES   (China)

Author keywords

Breeding; Genetic diversity; Genomics; Presence absence variants; Sorghum bicolour

Indexed keywords

DNA; GENE; GENETIC VARIATION; GENOME; PHENOTYPE; PLANT BREEDING; SORGHUM;

ARTICLE; BREEDING; CROSS BREEDING; DNA SEQUENCE; GENE ONTOLOGY; GENETIC VARIABILITY; GENETICS; GENOME SIZE; GENOMICS; INBREEDING; INHERITANCE; MOLECULAR GENETICS; PLANT CHROMOSOME; PLANT GENE; PLANT GENOME; PRESENCE/ABSENCE VARIANTS; RETROPOSON; SORGHUM; SORGHUM BICOLOUR; TRANSPOSON;

BREEDING; GENETIC DIVERSITY; GENOMICS; PRESENCE/ABSENCE VARIANTS; SORGHUM BICOLOUR;

CHROMOSOMES, PLANT; CROSSES, GENETIC; DNA TRANSPOSABLE ELEMENTS; GENE ONTOLOGY; GENES, PLANT; GENETIC VARIATION; GENOME SIZE; GENOME, PLANT; INBREEDING; INHERITANCE PATTERNS; MOLECULAR SEQUENCE ANNOTATION; RETROELEMENTS; SEQUENCE ANALYSIS, DNA; SORGHUM;

EID: 84892475088     PISSN: 16729072     EISSN: 17447909     Source Type: Journal    
DOI: 10.1111/jipb.12121     Document Type: Article

References (61)

1. Beló A, Beatty MK, Hondred D, Fengler KA, Li B, Rafalski A (2010) Allelic genome structural variations in maize detected by array comparative genome hybridization. Theor Appl Genet 120: 355-367
2. Berglund J, Nevalainen EM, Molin AM, Perloski M, Andre C, Zody MC, Sharpe T, Hitte C, Lindblad-Toh K, Lohi H (2012) Novel origins of copy number variation in the dog genome. Genome Biol 13: R73
3. Borevitz JO, Liang D, Plouffe D, Chang HS, Zhu T, Weigel D, Berry CC, Winzeler E, Chory J (2003) Large-scale identification of single-feature polymorphisms in complex genomes. Genome Res 13: 513-523
4. Borevitz JO, Hazen SP, Michael TP, Morris GP, Baxter IR, Hu TT, Chen H, Werner JD, Nordborg M, Salt DE (2007) Genome-wide patterns of single-feature polymorphism in Arabidopsis thaliana. Proc Natl Acad Sci USA 104: 12 057-12 062
5. Bradbury PJ, Zhang Z, Kroon DE, Casstevens TM, Ramdoss Y, Buckler ES (2007) TASSEL: Software for association mapping of complex traits in diverse samples. Bioinformatics 23: 2633-2635
6. Calviño M, Messing J (2012) Sweet sorghum as a model system for bioenergy crops. Curr Opin Biotechnol 23: 323-329
7. Candela H, Hake S (2008) The art and design of genetic screens: Maize. Nat Rev Genet 9: 192-203
8. Chia JM, Song C, Bradbury PJ, Costich D, de Leon N, Doebley J, Elshire RJ, Gaut B, Geller L, Glaubitz JC (2012) Maize HapMap2 identifies extant variation from a genome in flux. Nat Genet 44: 803-807
9. Conrad DF, Andrews TD, Carter NP, Hurles ME, Pritchard JK (2006) A high-resolution survey of deletion polymorphism in the human genome. Nat Genet 38: 75-81
10. Conrad DF, Pinto D, Redon R, Feuk L, Gokcumen O, Zhang Y, Aerts J, Andrews TD, Barnes C, Campbell P (2009) Origins and functional impact of copy number variation in the human genome. Nature 464: 704-712
11. Cook DE, Lee TG, Guo X, Melito S, Wang K, Bayless AM, Wang J, Hughes TJ, Willis DK, Clemente TE (2012) Copy number variation of multiple genes at Rhg1 mediates nematode resistance in Soybean. Science 338: 1206-1209
12. DeBolt S (2010) Copy number variation shapes genome diversity in Arabidopsis over immediate family generational scales. Genome Biol Evol 2: 441-453
13. de Cid R, Riveira-Munoz E, Zeeuwen PLJM, Robarge J, Liao W, Dannhauser EN, Giardina E, Stuart PE, Nair R, Helms C, Escaramis G, Ballana E, Martin-Ezquerra G, den Heijer M, Kamsteeg M, Joosten I, Eichler EE, Lazaro C, Pujol RM, Armengol L, Abecasis G, Elder JT, Novelli G, Armour JAL, Kwok P.-Y, Bowcock A, Schalkwijk J, Estivill X (2009) Deletion of the late cornified envelope LCE3B and LCE3C genes as a susceptibility factor for psoriasis. Nat Genet 41: 211-215
14. Doyle JJ (1987) A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochem Bull 19: 11-15
15. Du Z, Zhou X, Ling Y, Zhang Z, Su Z (2010) agriGO: A GO analysis toolkit for the agricultural community. Nucleic Acids Res 38: W64-W70
16. Durand E, Bouchet S, Bertin P, Ressayre A, Jamin P, Charcosset A, Dillmann C, Tenaillon MI (2012) Flowering time in maize: Linkage and epistasis at a major effect locus. Genetics 190: 1547-1562
17. Frazer KA, Chen XY, Hinds DA, Pant PVK, Patil N, Cox DR (2003) Genomic DNA insertions and deletions occur frequently between humans and nonhuman primates. Genome Res 13: 341-346
18. Gao Q, Yue G, Li W, Wang J, Xu J, Yin Y (2012) Recent progress using high-throughput sequencing technologies in plant molecular breeding. J Integr Plant Biol 54: 215-227
19. Hastings PJ, Lupski JR, Rosenberg SM, Ira G (2009) Mechanisms of change in gene copy number. Nat Rev Genet 10: 551-564
20. Hsing YI, Chern CG, Fan MJ, Lu PC, Chen KT, Lo SF, Sun PK, Ho SL, Lee KW, Wang YC (2007) A rice gene activation/knockout mutant resource for high throughput functional genomics. Plant Mol Biol 63: 351-364
21. Hurles ME, Dermitzakis ET, Tyler-Smith C (2008) The functional impact of structural variation in humans. Trends Genet 24: 238-245
22. Iafrate AJ, Feuk L, Rivera MN, Listewnik ML, Donahoe PK, Qi Y, Scherer SW, Lee C (2004) Detection of large-scale variation in the human genome. Nat Genet 36: 949-951
23. Itsara A, Cooper GM, Baker C, Girirajan S, Li J, Absher D, Krauss RM, Myers RM, Ridker PM, Chasman DI (2009) Population analysis of large copy number variants and hotspots of human genetic disease. Am J Hum Genet 84: 148-161
24. Kidd JM, Graves T, Newman TL, Fulton R, Hayden HS, Malig M, Kallicki J, Kaul R, Wilson RK, Eichler EE (2010) A human genome structural variation sequencing resource reveals insights into mutational mechanisms. Cell 143: 837-847
25. Korbel JO, Urban AE, Affourtit JP, Godwin B, Grubert F, Simons JF, Kim PM, Palejev D, Carriero NJ, Du L, Taillon BE, Chen Z, Tanzer A, Saunders ACE, Chi J, Yang F, 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: 420-426
26. Kumar R, Qiu J, Joshi T, Valliyodan B, Xu D, Nguyen HT (2007) Single feature polymorphism discovery in rice. PLoS ONE 2: e284
27. Lai J, Li R, Xu X, Jin W, Xu M, Zhao H, Xiang Z, Song W, Ying K, Zhang M (2010) Genome-wide patterns of genetic variation among elite maize inbred lines. Nat Genet 42: 1027-1030
28. Lam HYK, Mu XJ, Stuetz AM, Tanzer A, Cayting PD, Snyder M, Kim PM, Korbel JO, Gerstein MB (2009) Nucleotide-resolution analysis of structural variants using BreakSeq and a breakpoint library. Nat Biotechnol 28: 47-55
29. Lam HM, Xu X, Liu X, Chen W, Yang G, Wong FL, Li MW, He W, Qin N, Wang B (2010) Resequencing of 31 wild and cultivated soybean genomes identifies patterns of genetic diversity and selection. Nat Genet 42: 1053-1059
30. Liu G, Zhao SY, Bailey JA, Sahinalp SC, Alkan C, Tuzun E, Green ED, Eichler EE, Progm NCS (2003) Analysis of primate genomic variation reveals a repeat-driven expansion of the human genome. Genome Res 13: 358-368
31. Locke DP, Segraves R, Carbone L, Archidiacono N, Albertson DG, Pinkel D, Eichler EE (2003) Large-scale variation among human and great ape genomes determined by array comparative genomic hybridization. Genome Res 13: 347-357
32. Lu P, Han X, Qi J, Yang J, Wijeratne AJ, Li T, Ma H (2012) Analysis of Arabidopsis genome-wide variations before and after meiosis and meiotic recombination by resequencing Landsberg erecta and all four products of a single meiosis. Genome Res 22: 508-518
33. 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: 169-191
34. McCarroll SA, Altshuler DM (2007) Copy-number variation and association studies of human disease. Nat Genet 39: S37-S42
35. McCarroll SA, Huett A, Kuballa P, Chilewski SD, Landry A, Goyette P, Zody MC, Hall JL, Brant SR, Cho JH, Duerr RH, Silverberg MS, Taylor KD, Rioux JD, Altshuler D, Daly MJ, Xavier RJ (2008) Deletion polymorphism upstream of IRGM associated with altered IRGM expression and Crohn's disease. Nat Genet 40: 1107-1112
36. McDowell JM, Dhandaydham M, Long TA, Aarts MG, Goff S, Holub EB, Dangl JL (1998) Intragenic recombination and diversifying selection contribute to the evolution of downy mildew resistance at the RPP8 locus of Arabidopsis. Plant Cell 10: 1861-1874
37. 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: 1295-1308
38. Mills RE, Walter K, Stewart C, Handsaker RE, Chen K, Alkan C, Abyzov A, Yoon SC, Ye K, Cheetham RK (2011) Mapping copy number variation by population-scale genome sequencing. Nature 470: 59-65
39. Olson MV (1999) When less is more: Gene loss as an engine of evolutionary change. Am J Hum Genet 64: 18-23
40. 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-Rahman Ware D, Westhoff P, Mayer KFX, Messing J, Rokhsar DS, (2009) The Sorghum bicolor genome and the diversification of grasses. Nature 457: 551-556
41. Petrov DA (2002) Mutational equilibrium model of genome size evolution. Theor Popul Biol 61: 531-544
42. Price HJ, Dillon SL, Hodnett G, Rooney WL, Ross L, Johnston JS (2005) Genome evolution in the genus Sorghum (Poaceae). Ann Bot 95: 219-227
43. Salathia N, Lee HN, Sangster TA, Morneau K, Landry CR, Schellenberg K, Behere AS, Gunderson KL, Cavalieri D, Jander G (2007) Indel arrays: An affordable alternative for genotyping. Plant J 51: 727-737
44. Schnable JC, Freeling M, Lyons E (2012) Genome-wide analysis of syntenic gene deletion in the grasses. Genome Biol Evol 4: 265-277
45. Sebat J, Lakshmi B, Troge J, Alexander J, Young J, Lundin P, Maner S, Massa H, Walker M, Chi MY, Navin N, Lucito R, Healy J, Hicks J, Ye K, Reiner A, Gilliam TC, Trask B, Patterson N, Zetterberg A, Wigler M (2004) Large-scale copy number polymorphism in the human genome. Science 305: 525-528
46. Settles AM, Holding DR, Tan BC, Latshaw SP, Liu J, Suzuki M, Li L, O'Brien BA, Fajardo DS, Wroclawska E (2007) Sequence-indexed mutations in maize using the UniformMu transposon-tagging population. BMC Genomics 8: 116
47. Sharp AJ, Locke DP, McGrath SD, Cheng Z, Bailey JA, Vallente RU, Pertz LM, Clark RA, Schwartz S, Segraves R, Oseroff VV, Albertson DG, Pinkel D, Eichler EE (2005) Segmental duplications and copy-number variation in the human genome. Am J Hum Genet 77: 78-88
48. Springer NM, Ying K, Fu Y, Ji T, Yeh CT, Jia Y, Wu W, Richmond T, Kitzman J, Rosenbaum H (2009) Maize inbreds exhibit high levels of copy number variation (CNV) and presence/absence variation (PAV) in genome content. PLoS Genet 5: e1000734
49. Stahl EA, Dwyer G, Mauricio R, Kreitman M, Bergelson J (1999) Dynamics of disease resistance polymorphism at the Rpm1 locus of Arabidopsis. Nature 400: 667-671
50. 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: 1689-1699
51. Tan S, Zhong Y, Hou H, Yang S, Tian D (2012) Variation of presence/absence genes among Arabidopsis populations. BMC Evol Biol 12: 86
52. Tenaillon MI, Hollister JD, Gaut BS (2010) A triptych of the evolution of plant transposable elements. Trends Plant Sci 15: 471-478
53. Tittel-Elmer M, Bucher E, Broger L, Mathieu O, Paszkowski J, Vaillant I (2010) Stress-induced activation of heterochromatic transcription. PLoS Genet 6: e1001175
54. Tuzun E, Sharp AJ, Bailey JA, Kaul R, Morrison VA, Pertz LM, Haugen E, Hayden H, Albertson D, Pinkel D (2005) Fine-scale structural variation of the human genome. Nat Genet 37: 727-732
55. Vermerris W (2011) Survey of genomics approaches to improve bioenergy traits in maize, sorghum and sugarcane free access. J Integr Plant Biol 53: 105-119
56. Xie C, Mao X, Huang J, Ding Y, Wu J, Dong S, Kong L, Gao G, Li CY, Wei L (2011) KOBAS 2.0: A web server for annotation and identification of enriched pathways and diseases. Nucleic Acids Res 39: W316-W322
57. Yalcin B, Wong K, Agam A, Goodson M, Keane TM, Gan X, 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: 326-329
58. Ye J, Fang L, Zheng H, Zhang Y, Chen J, Zhang Z, Wang J, Li S, Li R, Bolund L, Wang J (2006) WEGO: A web tool for plotting GO annotations. Nucleic Acids Res 34: W293-W297
59. Yu CE, Dawson G, Munson J, D'Souza I, Osterling J, Estes A, Leutenegger AL, Flodman P, Smith M, Raskind WH, Spence MA, McMahon W, Wijsman EM, Schellenberg GD (2002) Presence of large deletions in kindreds with autism. Am J Hum Genet 71: 100-115
60. Yu P, Wang C, Xu Q, Feng Y, Yuan X, Yu H, Wang Y, Tang S, Wei X (2011) Detection of copy number variations in rice using array-based comparative genomic hybridization. BMC Genomics 12: 372
61. Zheng LY, Guo XS, He B, Sun LJ, Peng Y, Dong SS, Liu TF, Jiang S, Ramachandran S, Liu CM, Jing HC (2011) Genome-wide patterns of genetic variation in sweet and grain sorghum (Sorghum bicolor). Genome Biol 12: R114