Exploration of presence/absence variation and corresponding polymorphic markers in soybean genome

Journal of Integrative Plant Biology

Volumn 56, Issue 10, 2014, Pages 1009-1019

  Wang, Yufeng ^a   Lu, Jiangjie ^a   Chen, Shouyi ^b   Shu, Liping ^c   Palmer, Reid G ^d   Xing, Guangnan ^a   Li, Yan ^a   Yang, Shouping ^a   Yu, Deyue ^a   Zhao, Tuanjie ^a   Gai, Junyi ^a  

^a NANJING AGRICULTURAL UNIVERSITY   (China)

^b INSTITUTE OF GENETICS AND DEVELOPMENTAL BIOLOGY   (China)

^c BGIShenzhen ^*  (China)

^d IOWA STATE UNIVERSITY   (United States)

Author keywords

Polymorphism; Presence absence variation; Simple sequence repeat; Soybean; Whole genome sequence

Indexed keywords

DNA; GENETIC MARKER; GENOME; POLYMERASE CHAIN REACTION; POLYMORPHISM; SOYBEAN;

GLYCINE MAX;

MICROSATELLITE DNA;

GENETIC DATABASE; GENETIC POLYMORPHISM; GENETICS; PLANT GENOME; SOYBEAN;

DATABASES, GENETIC; GENOME, PLANT; MICROSATELLITE REPEATS; POLYMORPHISM, GENETIC; SOYBEANS;

EID: 84908330324     PISSN: 16729072     EISSN: 17447909     Source Type: Journal    
DOI: 10.1111/jipb.12208     Document Type: Article

References (59)

1. Abe J, Xu DH, Suzuki Y, Kanazawa A, Shimamoto Y (2003) Soybean germplasm pools in Asia revealed by nuclear SSRs. Theor Appl Genet 106: 445-453
2. Akkaya MS, Bhagwat AA, Cregan PB (1992) Length polymorphisms of simple sequence repeat DNA in soybean. Genetics 132: 1131- 1139
3. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215: 403-410
4. 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: 2581-2589
5. Batley J, Barker G, O'Sullivan H, Edwards KJ, Edwards D (2003) Mining for single nucleotide polymorphisms and insertions/deletions in maize expressed sequence tag data. Plant Physiol 132: 84-91
6. 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
7. Britten RJ, Rowen L, Williams J, Cameron RA (2003) Majority of divergence between closely related DNA samples is due to indels. Proc Natl Acad Sci USA 100: 4661-4665
8. Bryan GJ, Collins AJ, Stephenson P, Orry A, Smith JB, Gale MD (1997) Isolation and characterisation of microsatellites from hexaploid bread wheat. Theor Appl Genet 94: 557-563
9. Carter TE, Nelson RL, Sneller CH, Cui Z (2004) Genetic diversity in soybean. In: Boerma HR, Specht JE, eds. Soybeans: Improvement, Production, and Uses. American Society of Agronomy, Crop Science Society of America, and Soil Science Society of America, Madison, Wisconsin, Vol. Agronomy; no. 16. pp. 303-416
10. Choi IY, Hyten DL, Matukumalli LK, Song Q, Chaky JM, Quigley CV, Chase K, Lark KG, Reiter RS, Yoon MS, Hwang EY, Yi SI, Young ND, Shoemaker RC, van Tassell CP, Specht JE, Cregan PB (2007) A soybean transcript map: Gene distribution, haplotype and single-nucleotide polymorphism analysis. Genetics 176: 685-696
11. Cook DE, Lee TG, Guo X, Melito S, Wang K, Bayless AM, Wang J, Hughes TJ, Willis DK, Clemente TE, Diers BW, Jiang J, Hudson ME, Bent AF (2012) Copy number variation of multiple genes at Rhg1 mediates nematode resistance in soybean. Science 338: 1206-1209
12. Ding J, Araki H, Wang Q, Zhang P, Yang S, Chen JQ, Tian D (2007) Highly asymmetric rice genomes. BMC Genomics 8: 154
13. Doyle JJ, Doyle JL (1987) A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochem Bull 19: 11-15
14. 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
15. García-Lor A, Luro F, Navarro L, Ollitrault P (2012) Comparative use of InDel and SSR markers in deciphering the interspecific structure of cultivated citrus genetic diversity: A perspective for genetic association studies. Mol Genet Genomics 287: 77-94
16. Gill N, Findley S, Walling JG, Hans C, Ma J, Doyle J, Stacey G, Jackson SA (2009) Molecular and chromosomal evidence for allopolyploidy in soybean, Glycine max (L.) Merr. Plant Physiol 151: 1167-1174
17. Hao DR, Cheng H, Yin ZT, Cui SY, Zhang D, Wang H, Yu DY (2012) Identification of single nucleotide polymorphisms and haplotypes associated with yield and yield components in soybean (Glycine max) landraces across multiple environments. Theor Appl Genet 124: 447-458
18. Haun WJ, Hyten DL, Xu WW, Gerhardt DJ, Albert TJ, Richmond T, Jeddeloh JA, Jia G, Springer NM, Vance CP, Stupar RM (2011) The composition and origins of genomic variation among individuals of the soybean reference cultivar Williams 82. Plant Physiol 155: 645- 655
19. Hyten DL, Choi IY, Song Q, Specht JE, Carter TEJ, Shoemaker RC, Hwang EY, Matukumalli LK, Cregan PB (2010) A high density integrated genetic linkage map of soybean and the development of a 1536 universal soy linkage panel for quantitative trait locus mapping. Crop Sci 50: 960-968
20. Hyten DL, Song Q, Zhu Y, Choi IY, Nelson RL, Costa JM, Specht JE, Shoemaker RC, Cregan PB (2006) Impacts of genetic bottlenecks on soybean genome diversity. Proc Natl Acad Sci USA 103: 16666- 16671
21. 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
22. Keim P, Shoemaker RC, Palmer RG (1989) Restriction fragment length polymorphism diversity in soybean. Theor Appl Genet 77: 786-792
23. Kent WJ (2002) BLAT-the BLAST-like alignment tool. Genome Res 12: 656-664
24. Kern AD, Begun DJ (2008) Recurrent deletion and gene presence/ absence polymorphism: Telomere dynamics dominate evolution at the tip of 3L in Drosophila melanogaster and D. simulans. Genetics 179: 1021-1027
25. Kim MY, Lee S, Van K, Kim TH, Jeong SC, Choi IY, Kim DS, Lee YS, Park D, Ma J, Kim WY, Kim BC, Park S, Lee KA, Kim DH, Kim KH, Shin JH, Jang YE, Kim KD, Liu WX, Chaisan T, Kang YJ, Lee YH, Kim KH, Moon JK, Schmutz J, Jackson SA, Bhak J, Lee SH (2010) Whole-genome sequencing and intensive analysis of the undomesticated soybean (Glycine soja Sieb. and Zucc.) genome. Proc Natl Acad Sci USA 107: 22032-22037
26. Lam HM, Xu X, Liu X, Chen W, Yang G, Wong FL, Li MW, He W, Qin N, Wang B, Li J, Jian M, Wang J, Shao G, Wang J, Sun SS, Zhang G (2010) Resequencing of 31 wild and cultivated soybean genomes identifies patterns of genetic diversity and selection. Nat Genet 42: 1053-1059
27. Li RQ, Li YR, Zheng HC, Luo RB, Zhu HM, Li Q, Qian W, Ren Y, Tian G, Li J, Zhou G, Zhu X, Wu H, Qin J, Jin X, Li D, Cao H, Hu X, Blanche H, Cann H, Zhang X, Li S, Bolund L, Kristiansen K, Yang H, Wang J, Wang J (2010) Building the sequence map of the human pan-genome. Nat Biotechnol 28: 57-63
28. Li ZL, Nelson RL (2002) RAPD marker diversity among cultivated and wild soybean accessions from four Chinese provinces. Crop Sci 42: 1737-1744
29. Liu B, Wang Y, Zhai W, Deng J, Wang H, Cui Y, Cheng F, Wang XW, Wu J (2013) Development of InDel markers for Brassica rapa based on whole-genome re-sequencing. Theor Appl Genet 126: 231-239
30. Liu K, Muse SV (2005) PowerMarker: An integrated analysis environment for genetic marker analysis. Bioinformatics 21: 2128-2129
31. Maughan PJ, Saghi Maroof MA, Buss GR (1995) Microsatellite and amplified sequence length polymorphisms in cultivated and wild soybean. Genome 38: 715-723
32. Maughan PJ, Saghai Maroof MA, Buss GR, Huestis GM (1996) Amplified fragment length polymorphism (AFLP) in soybean: Species diversity, inheritance, and near-isogenic line analysis. Theor Appl Genet 93: 392-401
33. McCouch SR, Teytelman L, Xu Y, Lobos KB, Clare K, Walton M, Fu B, Maghirang R, Li Z, Xing Y, Zhang Q, Kono I, Yano M, Fjellstrom R, DeClerck G, Schneider D, Cartinhour S, Ware D, Stein L (2002) Development and mapping of 2240 new SSR markers for rice (Oryza sativa L.). DNA Res 9: 257-279
34. 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
35. 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: 997-1002
36. Morgante M, Olivieri AM (1993) PCR-amplified microsatellites as markers in plant genetics. Plant J 3: 175-182
37. Moriya Y, Itoh M, Okuda S, Yoshizawa AC, Kanehisa M (2007) KAAS: An automatic genome annotation and pathway reconstruction server. Nucleic Acids Res 35: W182-W185
38. Ohno S (1970) Evolution by Gene Duplication. Springer, Berlin, New York
39. Ollitrault F, Terol J, Martin AA, Pina JA, Navarro L, Talon M, Ollitrault P (2012) Development of indel markers from Citrus clementina (Rutaceae) BAC-end sequences and interspecific transferability in Citrus. Am J Bot 99: e268-e273
40. Roder MS, Plaschke J, Konig SU, Borner A, Sorrells ME, Tanksley SD, Ganal MW (1995) Abundance, variability and chromosomal location of microsatellites in wheat. Mol General Genet 246: 327-333
41. Rozen S, Skaletsky H (2000) Primer3 on the WWW for general users and for biologist programmers. Methods Mol Biol 132: 365- 386
42. Schmutz J, Cannon SB, Schlueter J, Ma J, Mitros T, Nelson W, Hyten DL, Song Q, Thelen JJ, Cheng J, Xu D, Hellsten U, May GD, Yu Y, Sakurai T, Umezawa T, Bhattacharyya MK, Sandhu D, Valliyodan B, Lindquist E, Peto M, Grant D, Shu S, Goodstein D, Barry K, Futrell- Griggs M, Abernathy B, Du J, Tian Z, Zhu L, Gill N, Joshi T, Libault M, Sethuraman A, Zhang XC, Shinozaki K, Nguyen HT, Wing RA, Cregan P, Specht J, Grimwood J, Rokhsar D, Stacey G, Shoemaker RC, Jackson SA (2010) Genome sequence of the palaeopolyploid soybean. Nature 463: 178-183
43. Shultz J, Kazi S, Bashir R, Afzal J, Lightfoot D (2007) The development of BAC-end sequence-based microsatellite markers and placement in the physical and genetic maps of soybean. Theor Appl Genet 114: 1081-1090
44. Skorupska HT, Shoemaker RC, Warner A, Shipe ER, Bridges WC (1993) Restriction fragment length polymorphism in soybean germplasm of the southern USA. Crop Sci 33: 1169-1176
45. Song QJ, Hyten DL, Jia GF, Quigley CV, Fickus EW, Nelson RL, Cregan PB (2013) Development and evaluation of SoySNP50K, a high-density genotyping array for soybean. PLoS ONE 8: e54985
46. Song QJ, Jia GF, Zhu YL, Grant D, Nelson RT, Hwang EY, Hyten DL, Cregan PB (2010) Abundance of SSR motifs and development of candidate polymorphic SSR markers (BARCSOYSSR_1.0) in soybean. Crop Sci 50: 1950-1960
47. Springer NM, Ying K, Fu Y, Ji T, 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: e1000734
48. Temnykh S, William DP, Nicola A, Sam C, Hauck N, Lipovich L, Cho YG, Ishii T, McCouch SR (2000) Mapping and genome organization of microsatellite sequences in rice (Oryza sativa L.). Theor Appl Genet 100: 697-712
49. Thompson JA, Nelson RL (1998) Core set of primers to evaluate genetic diversity in soybean. Crop Sci 38: 1356-1362
50. Ude GN, Kenworthy WJ, Costa JM, Cregan PB, Alvernaz J (2003) Genetic diversity of soybean cultivars from China, Japan, North America, and North American ancestral lines determined by amplified fragment length polymorphism. Crop Sci 43: 1858-1867
51. Varshney R, Graner A, Sorrells M (2005) Genic microsatellite markers in plants: Features and applications. Trends Biotechnol 23: 48-55
52. Vos P, Hogers R, Bleeker M, Reijans M, Lee T, Hornes M, Friters A, Pot J, Paleman J, Kuiper M, Zabeau M (1995) AFLP: A new technique for DNA fingerprinting. Nucleic Acids Res 23: 4407-4414
53. Welsh J, McClelland M (1990) Fingerprinting genomes using PCR with arbitrary primers. Nucleic Acids Res 18: 7213-7218
54. 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
55. Yu J, Wang J, Lin W, Li S, Li H, Zhou J, Ni P, Dong W, Hu S, Zeng C, Zhang J, Zhang Y, Li R, Xu Z, Li X, Zheng H, Cong L, Lin L, Yin J, Geng J, Li G, Shi J, Liu J, Lv H, Li J, Deng Y, Ran L, Shi X, Wang X, Wu Q, Li C, Ren X, Li D, Liu D, Zhang X, Ji Z, Zhao W, Sun Y, Zhang Z, Bao J, Han Y, Dong L, Ji J, Chen P, Wu S, Xiao Y, Bu D, Tan J, Yang L, Ye C, Xu J, Zhou Y, Yu Y, Zhang B, Zhuang S, Wei H, Liu B, Lei M, Yu H, Li Y, Xu H, Wei S, He X, Fang L, Huang X, Su Z, Tong W, Tong Z, Ye J, Wang L, Lei T, Chen C, Chen H, Huang H, Zhang F, Li N, Zhao C, Huang Y, Li L, Xi Y, Qi Q, Li W, Hu W, Tian X, Jiao Y, Liang X, Jin J, Gao L, Zheng W, Hao B, Liu S, Wang W, Yuan L, Cao M, McDermott J, Samudrala R, Wong GK, Yang H (2005) The genomes of Oryza sativa: A history of duplications. PLoS Biol 3: e38
56. Zhang JZ (2003) Evolution by gene duplication: an update. Trends Ecol Evol 18: 292-298
57. Zhang LM, Luo H, Liu ZQ, Zhao Y, Luo JC, Hao DY, Jing HC (2013) Genome-wide patterns of large-size presence/absence variants in sorghum. J Integr Plant Biol 56: 24-37
58. 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 bicolor). Genome Biol 12: R114
59. 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: 3189-3201