An analysis of population structure and linkage disequilibrium using multilocus data in 187 maize inbred lines

Molecular Breeding

Volumn 21, Issue 4, 2008, Pages 407-418

  Xie, Chuanxiao ^a   Warburton, Marilyn ^b   Li, Mingshun ^a   Li, Xinhai ^a   Xiao, Muji ^a   Hao, Zhuanfang ^a   Zhao, Qi ^c   Zhang, Shihuang ^a  

^a INSTITUTE OF PLANT PROTECTION   (China)

^b INTERNATIONAL MAIZE AND WHEAT IMPROVEMENT CENTER CIMMYT   (Mexico)

^c CAPITAL NORMAL UNIVERSITY   (China)

Author keywords

Association mapping; Linkage disequilibrium; Maize (Zea mays L.); Population structure

Indexed keywords

DNA SEQUENCES; GENES; GRAIN (AGRICULTURAL PRODUCT); POPULATION STATISTICS;

ASSOCIATION MAPPING; GENETICS DIVERSITIES; GERMPLASMS; INBRED LINE; LANDRACES; LINKAGE DISEQUILIBRIUM; MAIZE (ZEA MAY L); MAIZE (ZEA MAYS L.); MAIZE INBREDS; POPULATION STRUCTURES;

MAPPING;

ZEA MAYS;

EID: 41549137820     PISSN: 13803743     EISSN: None     Source Type: Journal    
DOI: 10.1007/s11032-007-9140-8     Document Type: Article

References (42)

1. Andersen JR, Schrag T, Melchinger AE, Zein I, Lubberstedt T (2005) Validation of Dwarf8 polymorphisms associated with flowering time in elite European inbred lines of maize (Zea mays L.). Theor Appl Genet 111:206-217
2. Camus-Kulandaivelu L, Veyrieras J, Madur D, Combes V, Fourmann M, Barraud S, Dubreuil P, Gouesnard B, Manicacci D, Charcosset A (2006) Maize adaptation to temperate climate: relationship between population structure and polymorphism in the Dwarf8 gene. Genetics 172:2449-2463
3. Chao SM, Zhang WJ, Dubcovsky J, Sorrells M (2007) Evaluation of genetic diversity and genome-wide linkage disequilibrium among U.S. wheat (Triticum aestivum L.) germplasm representing different market classes. Crop Sci 47(3):1018-1030
4. Charcosset A, Essioux L (1994) The effect of population structure on the relationship between heterosis and heterozygosity at marker loci. Theor Appl Genet 89:336-343
5. Doebley J, Wendel JF, Smith JSC, Stuber CW, Goodman MM (1988) The origin of corn belt maize: the isozyme evidence. Econ Bot 42:120-131
6. Excoffier L (2001) Analysis of population subdivision. In: Balding D, Bishop M, Cannings C (eds) Handbook of Statistical Genetics. John Wiley & Sons, New York, pp 271-307
7. Falush D, Stephens M, Pritchard JK (2003) Inference of population structure using multilocus genotype data: linked loci and correlated allele frequencies. Genetics 164:1567-1587
8. Flint-Garcia SA, Thornsberry JM, Buckler ES (2003) Structure of linkage disequilibrium in plants. Annu Rev Plant Biol 54:357-374
9. Flint-Garcia SA, Thuillet AC, Yu J, Pressoir G, Romero SM, Mitchell SE, Doebley J, Kresovich S, Goodman MM, Buckler ES (2005) Maize association population: a high-resolution platform for quantitative trait locus dissection. Plant J 44(6):1054-64
10. Garris AJ, Tai TH, Coburn J, Kresovich S, McCouch S (2005) Genetic structure and diversity in Oryza sativa L. Genetics 169:1631-1638
11. Kraakman ATW, Niks RE, Van den Berg PMMM, Stam P, Van Eeuwijk FA (2004) Linkage disequilibrium mapping of yield and yield stability in modern spring barley cultivars. Genetics 168:435-446
12. Li XH, Fu JH, Zhang SH, Yuan LX, Li MS (2000) Genetic variation of inbred lines of maize detected by SSR markers. Sci Agric Sin 33:1-9
13. Li Y (1998) Development and germplasm base of maize hybrids in China. Maydica 43:259-269
14. Li Y, Du J, Wang T, Shi Y, Song Y, Jia J (2002) Genetic diversity and relationships among Chinese maize inbred lines revealed by SSR markers. Maydica 47:93-101
15. Liu K, Goodman M, Muse S, Smith JS, Buckler E, Doebley J (2003) Genetic structure and diversity among maize inbred lines as inferred from DNA microsatellites. Genetics 165:2117-2128
16. Lu H, Bernardo R (2001) Molecular marker diversity among current and historical maize inbreds. Theor Appl Genet 103:613-617
17. Lu H, Redus, MA, Coburn JR, Rutger JN, McCouch SR, Tai TH (2005) Population structure and breeding patterns of 145 U.S. rice cultivars based on SSR marker analysis. Crop Sci 45(1):66-76
18. Malysheva-Otto LV, Ganal MW, Röder MS (2006) Analysis of molecular diversity, population structure and linkage disequilibrium in a worldwide survey of cultivated barley germplasm (Hordeum vulgare L.) BMC. Genetics 7:6
19. Nordborg M, Borevitz JO, Bergelson J, Berry CC, Chory J, Hagenblad J, Kreitman M, Maloof JN, Noyes T, Oefner PJ, Stahl EA, Weigel D (2002) The extent of linkage disequilibrium in Arabidopsis thaliana. Nat Genet 30:190-193
20. Palaisa K, Morgante M, Tingey S, Rafalski A. (2004) Long-range patterns of diversity and linkage disequilibrium surrounding the maize Y1 gene are indicative of an asymmetric selective sweep. Proc Natl Acad Sci USA 101: 9885-9890
21. Pejic I, Ajmore-Marsan P, Morgante M, Kozumplick V, Castiglioni P, Taramino G, Motto M (1998) Comparative analysis of genetic similarity among maize inbred lines detected by RFLPs, RAPDs, SSRs, and AFLPs. Theor Appl Genet 97:1248-1255
22. Pritchard JK (2001) Deconstructing maize population structure. Nat Genet 28(3):286-289
23. Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics 155:945-959
24. Rafalski JA, Vogel JM, Morgante M, Powell W, Andre C, Tingey SV (1996) Generating and using DNA markers in plants. In: Birren B, Lai E (eds), Non-mammalian genomic analysis. A practical guide. Academic Press, San Diego, pp 75-134
25. Reif JC, Warburton ML, Xia XC, Hoisington DA, Crossa J, Taba S, Muminović J, Bohn M, Frisch M, Melchinger AE (2006) Grouping of accessions of Mexican races of maize revisited with SSR markers. Theor Appl Genet 113:177-185
26. Remington DL, Thornsberry JM, Matsuoka Y, Wilson LM, Whitt SR, Doebley J, Kresovich S, Goodman MM, Buckler ES (2001) Structure of linkage disequilibrium and phenotypic associations in the maize genome. Proc Natl Acad Sci USA 98:11479-11484
27. Saghai-Maroof MA, Soliman K, Jorgensen RA, Allard RW (1984) Ribosomal DNA spacer length polymorphism in barley: Mendelian inheritance, chromosomal location and population dynamics. Proc Natl Acad Sci USA 81:8014-8018
28. Senior ML, Murphy JP, Goodman MM, Stuber CW (1998) Utility of SSRs for determining genetic similarities and relationships in maize using an agarose gel system. Crop Sci 38:1088-1098
29. Smith JSC, Chin ECL, Shu H, Smith OS, Wall SJ, Senior ML, Mitchell SE, Kresovich S, Ziegle J (1997) An evaluation of the utility of SSR loci as molecular markers in maize (Zea mays L): comparisons with data from RFLPS and pedigree. Theor Appl Genet 95:163-173
30. Smith OS, Smith JSC (1992) Measurement of genetic diversity among maize hybrids - a comparison of isozymic, RFLP, pedigree, and heterosis data. Maydica 37:53-60
31. Stich B, Melchinger AE, Frisch M, Maurer HP, Hecknberger M, Reif JC (2005) Linkage disequilibrium in European elite maize germplasm investigated with SSRs. Theor Appl Genet 111:723-730
32. Szalma SJ, Buckler ES, Snook ME, McMullen MD (2005) Association analysis of candidate genes for maysin and chlorogenic acid accumulation in maize silks. Theor Appl Genet 110:1324-1333
33. Tenaillon MI, Sawkins MC, Long AD, Gaut RL, Doebley JF, Gaut BS (2001) Patterns of DNA sequence polymorphism along chromosome 1 of maize (Zea mays ssp. mays L.) Proc Natl Acad Sci USA 98:9161-9166
34. Thornsberry JM, Goodman MM, Doebley J, Kresovich S, Nielsen D, Buckler ES (2001) Dwarf8 polymorphisms associate with variation in flowering time. Nat Genet 28:286-89
35. Vigouroux Y, Mitchell S, Matsuoka Y, Hamblin M, Kresovich S, Smith JSC, Jaqueth J, Smith OS, Doebley J (2005) An analysis of genetic diversity across the maize genome using microsatellites. Genetics 169:1617-1630
36. Warburton ML, Ribaut JM, Franco J, Crossa J, Dubreuil P, Betrán FJ (2005) Genetic characterization of 218 elite CIMMYT inbred maize lines using RFLP markers. Euphytica 142:97-106
37. Wilson LM, Whitt SR, Ibáñez AM, Rocheford TR, Goodman MM, Buckler ES (2004) Dissection of Maize Kernel Composition and Starch Production by Candidate Gene Association. Plant Cell 16:2719-2733
38. Wright S (1951) The genetical structure of population. Ann Eugen 15:323-354
39. Xia XC, Reif JC, Melchinger AE, Frisch M, Hoisington DA, Beck D, Warburton ML (2005) Genetic diversity among CIMMYT maize inbred lines investigated with SSR markers: II. Subtropical, tropical mid-altitude, and highland maize inbred lines and their relationships with elite U.S. and European maize. Crop Sci 45(6):2573-2582
40. Yu J, Buckler ES (2006) Genetic association mapping and genome organization of maize. Curr Opin Biotechnol 17:155-160
41. Yu J, Pressoir G, Briggs WH, Bi IV, Yamasaki M, Doebley JF, McMullen MD, Gaut BS, Nielsen DM, Holland JB, Kresovich S, Buckler ES (2006) A unified mixed-model method for association mapping that accounts for multiple levels of relatedness. Nat Genet 38:203-208
42. Yuan LX, Fu JH, Warburton LM, Li XH, Zhang SH, Khairallah M, Liu Z X, Peng ZB, Li LC (2000) Comparison of gentic diversity in maize inbreds based on RFLP, SSR, AFLP and RAPD markers. Acta Genet Sin 27:725-733