Population structure and linkage disequilibrium of ICRISAT foxtail millet (Setaria italica (L.) P. Beauv.) core collection

Euphytica

Volumn 196, Issue 3, 2014, Pages 423-435

  Vetriventhan, M ^a   Upadhyaya, Hari D ^a   Anandakumar, C R ^b   Senthilvel, S ^a,d   Varshney, R K ^a   Parzies, Heiko K ^c  

^a INTERNATIONAL CROPS RESEARCH INSTITUTE FOR THE SEMI ARID TROPICS ICRISAT   (India)

^b TAMIL NADU AGRICULTURAL UNIVERSITY   (India)

^c UNIVERSITY OF HOHENHEIM   (Germany)

^d DIRECTORATE OF OILSEEDS RESEARCH   (India)

Author keywords

Analysis of molecular variance; Core collection; Foxtail millet; Genetic diversity; Linkage disequilibrium; Population structure; Simple sequence repeat

Indexed keywords

SETARIA ITALICA;

EID: 84897609694     PISSN: 00142336     EISSN: 15735060     Source Type: Journal    
DOI: 10.1007/s10681-013-1044-6     Document Type: Article

References (66)

1. Abdurakhmonov IY, Abdukarimov A (2008) Application of association mapping to understating the genetic diversity of plant genetic resources. Int J Plant Genomics. doi: 10. 1155/2008/574927.
2. Agrama HA, Eizenga GC, Yan W (2007) Association mapping of yield and its components in rice cultivars. Mol Breed 19: 341-356.
3. Austin DF (2006) Foxtail millets (Setaria: Poaceae)-abandoned food in two hemispheres. Econ Bot 60: 143-158.
4. Barton L, Newsome SD, Fa-Hu Chen, Wang H, Guilderson TP, Bettinger RL (2009) Agricultural origins and the isotopic identity of domestication in northern China. PNAS 106: 5523-5528.
5. Bennetzen JL, Schmutz J, Wang H et al (2012) Reference genome sequence of the model plant Setaria. Nat Biotechnol 30: 555-561.
6. Blair MW, Díaz LM, Buendía HF, Duque MC (2009) Genetic diversity, seed size associations and population structure of a core collection of common beans (Phaseolus vulgaris L.). Theor Appl Genet 119: 955-972.
7. Borba TCO, Brondani RPV, Breseghello F, Coelho ASG, Mendonça JA, Rangel PHN, Brondani C (2010) Association mapping for yield and grain quality traits in rice (Oryza sativa L.). Genet Mol Biol 33: 515-524.
8. 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.
9. Dodig D, Zoric M, Kobiljski B, Savic J, Kandic V, Quarrie S, Barnes J (2012) Genetic and association mapping study of wheat agronomic traits under contrasting water regimes. Int J Mol Sci 13: 6167-6188.
10. Doust AN, Kellogg EA, Devos KM, Bennetzen JL (2009) Foxtail millet: a sequence driven grass model system. Plant Physiol 149: 137-141.
11. Flint-Garcia SA, Thuillet AC, Yu JM, 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: 1054-1064.
12. Frankel OH (1984) Genetic perspective of germplasm conservation. In: Arber W, Illmensee K, Peacock WJ, Starlinger P (eds) Genetic manipulations: impact of man and society. Cambridge University Press, Cambridge, pp 161-170.
13. Hirano R, Naito K, Fukunaga K, Watanabe KN, Ohsawa R, Kawase M (2011) Genetic structure of landraces in foxtail millet (Setaria italica (L.) P. Beauv.) revealed with transposon display and interpretation to crop evolution of foxtail millet. Genome 54: 498-506.
14. Holland JB (2007) Genetic architecture of complex traits in plants. Curr Opin Plant Biol 10: 156-161.
15. Jia X, Zhang Z, Liu Y, Zhang C, Shi Y, Song Y, Wang T, Li Y (2009) Development and genetic mapping of SSR markers in foxtail millet (Setaria italica (L.) P. Beauv.). Theor Appl Genet 118: 821-829.
16. Jia G, Shi S, Wang C, Niu Z, Chai Y, Zhi H, Diao X (2013a) Molecular diversity and population structure of Chinese green foxtail [Setaria viridis (L.) Beauv.] revealed by microsatellite analysis. J Exp Bot 64: 3645-3655.
17. Jia G, Huang X, Zhi H, Zhao Y et al (2013b) A haplotype map of genomic variations and genome-wide association studies of agronomic traits in foxtail millet (Setaria italica). Nat Genet 45: 957-961.
18. Jun TH, van K, Kim MY, Lee SH, Walker DR (2008) Association analysis using SSR markers to find QTL for seed protein content in soybean. Euphytica 162: 179-191.
19. Kihara H, Kishimoto E (1942) Bastrade zwischen Setaria italica und S. viridis. (in Japanese with German summary). Bot Mag Tokyo 56: 62-67.
20. 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.
21. Kruglyak L (1999) Prospects for whole-genome linkage disequilibrium mapping of common disease genes. Nat Genet 22: 139-144.
22. Kumar R, Qiu J, Joshi T, Valliyodan B, Xu D, Nguyen HT (2007) Single feature polymorphism discovery in rice. PLoS One 2: e284.
23. Kumari K, Muthamilarasan M, Misra G, Gupta S, Subramanian A, Parida SK, Chattopadhyay D, Prasad M (2013) Development of eSSR-Markers in Setariaitalica and their applicability in studying genetic diversity, cross-transferability and comparative mapping in millet and non-millet species. PLoS One 8(6): e67742. doi: 10. 1371/journal. pone. 0067742.
24. Li P, Brutnell TP (2011) Setariaviridis and Setariaitalica, model genetic systems for the panicoid grasses. J Exp Bot 62: 3031-3037.
25. Li HW, Li CH, Pao WK (1945) Cytological and genetical studies of the interspecific cross of cultivated foxtail millet, Setaria italica (L.) Beauv., and the green foxtail millet, S. viridis (L.). J Am Soc Agron 37: 32-54.
26. Lin HS, Liao GI, Chiang CY, Kuoh CS, Chang SB (2012) Genetic diversity in the foxtail millet (Setaria italica) germplasm as determined by agronomic traits and microsatellite markers. Aust J Crop Sci 6(2): 342-349.
27. Liu K, Muse SV (2005) Powermarker: an integrated analysis environment for genetic marker data. Bioinformatics 21: 2128-2129.
28. Liu L, Wang L, Yao J, Zhang Y, Zhao C (2010) Association mapping of six agronomic traits on chromosome 4A of wheat (Triticum aestivum L.). Mol Pl Breed 1(5): 10.
29. Liu Z, Bai G, Zhang D, Znu C, Xia X, Cheng Z, Shi Z (2011) Genetic diversity and population structure of elite foxtail millet (Setaria italica (L.) P. Beauv.) germplasm in China. Crop Sci 51: 1655-1663.
30. Lu H, Zhang J, Liu KB, Wu N, Li Y, Zhou K, Ye M, Zhang T, Zhang H, Yang X, Shen L, Xu D, Li Q (2009) Earliest domestication of common millet (Panicum miliaceum) in East Asia extended to 10, 000 years ago. PNAS 106: 7367-7372.
31. Mace ES, Buhariwalla HK, Crouch JH (2003) A high-throughput DNA extraction protocol for tropical molecular breeding programs. Plant Mol Biol Repor 21: 459a-459h.
32. Malosetti M, van der Linden CG, Vosman B, van Eeuwijk FA (2007) A mixed-model approach to association mapping using pedigree information with an illustration of resistance to Phytophthora infestans in potato. Genetics 175: 879-889.
33. Murray SC, Rooney WL, Hamblin MT, Mitchell SE, Kresovich S (2009) Sweet sorghum genetic diversity and association mapping for brix and height. Plant Genome 2: 48-62.
34. Muthamilarasan M, Venkata Suresh B, Pandey G, Kumari K, Kumar Parida S, Prasad M (2013) Development of 5123 intron-length polymorphic markers for large-scale genotyping applications in foxtail millet. DNA Res. doi: 10. 1093/dnares/dst039.
35. Nei M (1972) Genetic distance between populations. Am Nat 106: 283-392.
36. Nei M (1973) Analysis of gene diversity in subdivided populations. PNAS 70: 3321-3323.
37. Neumann K, Kobiljski B, Denčić S, Vershney RK, Börner A (2011) Genome-wide association mapping: a case study in bread wheat (Triticum aestivum L.). Mol Breed 27: 37-58.
38. 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.
39. Pandey G, Misra G, Kumari K, Gupta S, Parida SK, Chattopadhyay D, Prasad M (2013) Genome-wide development and use of microsatellite markers for large-scale genotyping applications in foxtail millet [Setaria italica (L.)]. DNA Res 20: 197-207.
40. GENALEX 6: genetic analysis in Excel. Population genetic software for teaching and research. Mol Ecol Notes 6(1): 288-295.
41. Peleg Z, Fahima T, Abbo S, Krugman T, Saranga Y (2008a) Genetic structure of wild emmer wheat populations as reflected by transcribed versus anonymous SSR markers. Genome 51: 187-195.
42. Peleg Z, Saranga Y, Krugman T, Abbo S, Nevo E, Fahima T (2008b) Allelic diversity associated with aridity gradient in wild emmer wheat populations. Plant Cell Environ 31: 39-49.
43. Perrier X and Jacquemoud-Collet JP (2006) DARwin software (2006) http://darwin. cirad. fr/darwin.
44. Prasada Rao KE, de Wet JMJ, Brink DK, Mengesha MH (1987) Intraspecific variation and systematics of cultivated Setaria italica, foxtail millet (Poaceae). Econ Bot 41: 108-116.
45. Pritchard JK, Stephens M, Rosenberg NA, Donnelly P (2000a) Association mapping in structured populations. Am J Hum Genet 67: 170-181.
46. Pritchard JK, Stephens M, Donnelly P (2000b) Inference of population structure using multilocus genotype data. Genetics 155: 945-959.
47. Remington DL, Thornsberry JM, Matsuoka Y, Wilson LM, Whitt SR, Doebley J, Kresovich S, Goodman MM, Buckler ES IV (2001) Structure of linkage disequilibrium and phenotypic associations in the maize genome. PNAS 98: 11479-11484.
48. Shehzad T, Iwata H, Okuno K (2009) Genome-wide association mapping of quantitative traits in sorghum (Sorghum bicolor (L.) Moench) by using multiple models. Breed Sci 59: 217-227.
49. Stich B, Melchinger AE, Frisch M, Maurer HP, Heckenberger M, Reifl JC (2005) Linkage disequilibrium in European elite maize germplasm investigated with SSRs. Theor Appl Genet 111: 723-730.
50. Tao YZ, Henzell RG, Jordan DR, Butler DG, Kelly AM, McIntyre CL (2000) Identification of genomic regions associated with stay green in sorghum by testing RILs in multiple environments. Theor Appl Genet 100: 1225-1232.
51. Upadhyaya HD, Ortiz R (2001) A mini core subset for capturing diversity and promoting utilization of chickpea genetic resources in crop improvement. Theor Appl Genet 102: 1292-1298.
52. Upadhyaya HD, Pundir RPS, Gowda CLL, Reddy VG, Singh S (2008) Establishing a core collection of foxtail millet to enhance utilization of germplasm of an underutilized crop. Plant Genet Resour 7: 177-184.
53. Upadhyaya HD, Yi-Hong Wang, Shivali Sharma, Singh S (2012a) Association mapping of height and maturity across five environments using sorghum mini core collection. Genome 55: 471-479.
54. Upadhyaya HD, Yi-Hong Wang, Shivali Sharma, Singh S, Hasenstein KH (2012b) SSR markers linked to kernel weight and tiller number in sorghum identified by association mapping. Euphytica 187: 401-410.
55. Vetriventhan M, Upadhyaya HD, Anandakumar CR, Senthilvel S, Parzies HK, Bharathi A, Varshney RK, Gowda CLL (2012) Assessing genetic diversity, allelic richness and genetic relationship among races in ICRISAT foxtail millet core collection. Plant Genet Resour 10: 214-223.
56. Wang R, Yu Y, Zhao J, Shi Y, Song Y, Wang T, Li Y (2008) Population structure and linkage disequilibrium of a mini core set of maize inbred lines in China. Theor Appl Genet 117: 1141-1153.
57. Wang C, Chen J, Zhi H, Yang L, Li W, Wang Y, Li H, Zhao B, Chen M, Diao X (2010) Population genetics of foxtail millet and its wild ancestor. BMC Genet 11: 90.
58. Wang C, Jia G, Zhi H, Niu Z, Chai Y, Li W, Wang Y, Li H, Lu P, Zhao B, Diao X (2012) Genetic diversity and population structure of Chinese foxtail millet [Setariaitalica (L.) Beauv.] landraces. Gene Genome Genet 2: 769-777.
59. Wen W, Mei H, Feng F, Yu S, Huang Z, Wu J, Chen L, Xu X, Luo L (2009) Population structure and association mapping on chromosome 7 using a diverse panel of Chinese germplasm of rice (Oryza sative L.). Theor Appl Genet 119: 459-470.
60. Whitt SR, Buckler ES (2003) Using natural allelic diversity to evaluate gene function. Methods Mol Biol 236: 123-139.
61. Yang X, Yan J, Shah T, Warburton ML, Li Q, Li L, Chai YG, Fu Z, Zhou Y, Xu S, Bai G, Meng Y, Zheng Y, Li J (2010) Genetic analysis and characterization of a new maize association mapping panel for quantitative trait loci dissection. Theor Appl Genet 121: 417-431.
62. Yu J, Buckler ES (2006) Genetic association mapping and genome organization of maize. Curr Opin Biotech 17: 155-160.
63. Zhang P, Li J, Li X, Liu X, Zhao X, Lu Y (2011) Population structure and genetic diversity in a rice core collection (Oryza sativa L.) investigated with SSR markers. PLoS One 6: e27565.
64. Zhang G, Liu X, Quan Z et al (2012) Genome sequence of foxtail millet (Setaria italica) provides insights into grass evolution and biofuel potential. Nat Biotech 30: 549-554.
65. Zhao K, Aranzana MJ, Kim S, Lister C, Shindo C, Tang C, Toomajian C, Zheng H, Dean C, Marjoram P, Nordborg M (2007) An Arabidopsis example of association mapping in structured samples. PLoS Genet 3(1): e4.
66. Zhu CS, Gore M, Buckler ES, Yu JM (2008) Status and prospects of association mapping in plants. Plant Genome 1: 5-20.