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

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Abstract

Use of diverse germplasm is a key factor which allows high level of resolution due to extensive recombination in the history. Therefore, population used in association mapping should posses as many phenotypes as possible. One of the methods to obtain most of the phenotypes is to construct the core collection. The ICRISAT foxtail millet core collection consisting of 155 accessions was genotyped using 72 simple sequence repeat (SSR) markers to investigate the genetic diversity, population structure and linkage disequilibrium (LD). A high degree of molecular diversity among the accessions was found, with an average of 16.69 alleles per locus. STRUCTURE analyses classify the accessions into four subpopulations (SP) based on SSR allelic diversity. The Neighbor joining clustering and the principal coordinate analysis were in accordance with the racial classification. The distribution of molecular genetic variation among and within the four SP and three races showed high degree of variability within each group, and low level of genetic distance (GD) among the groups. LD decay of <40 cM of GD in foxtail millet core collection was observed, which suggests that it could be possible to achieve resolution down to the 40 cM level. From this investigation, it is evident that the foxtail millet core collection developed at ICRISAT is very diverse and could be a valuable resource for trait association mapping, crop breeding and germplasm management.

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References

  • 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

    PubMed Central  PubMed  Google Scholar 

  • Agrama HA, Eizenga GC, Yan W (2007) Association mapping of yield and its components in rice cultivars. Mol Breed 19:341–356

    Article  Google Scholar 

  • Austin DF (2006) Foxtail millets (Setaria: Poaceae)—abandoned food in two hemispheres. Econ Bot 60:143–158

    Article  Google Scholar 

  • 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

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Bennetzen JL, Schmutz J, Wang H et al (2012) Reference genome sequence of the model plant Setaria. Nat Biotechnol 30:555–561

    Article  CAS  PubMed  Google Scholar 

  • 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

    Article  CAS  PubMed  Google Scholar 

  • 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

    Article  Google Scholar 

  • 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

    Article  CAS  PubMed  Google Scholar 

  • 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

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Doust AN, Kellogg EA, Devos KM, Bennetzen JL (2009) Foxtail millet: a sequence driven grass model system. Plant Physiol 149:137–141

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • 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

    Article  CAS  PubMed  Google Scholar 

  • 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

    Google Scholar 

  • 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

    Article  CAS  PubMed  Google Scholar 

  • Holland JB (2007) Genetic architecture of complex traits in plants. Curr Opin Plant Biol 10:156–161

    Article  CAS  PubMed  Google Scholar 

  • 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

    Article  CAS  PubMed  Google Scholar 

  • 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

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • 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

    Article  CAS  PubMed  Google Scholar 

  • 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

    Article  CAS  Google Scholar 

  • Kihara H, Kishimoto E (1942) Bastrade zwischen Setaria italica und S. viridis. (in Japanese with German summary). Bot Mag Tokyo 56:62–67

    Google Scholar 

  • 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

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Kruglyak L (1999) Prospects for whole-genome linkage disequilibrium mapping of common disease genes. Nat Genet 22:139–144

    Article  CAS  PubMed  Google Scholar 

  • Kumar R, Qiu J, Joshi T, Valliyodan B, Xu D, Nguyen HT (2007) Single feature polymorphism discovery in rice. PLoS One 2:e284

    Article  PubMed Central  PubMed  Google Scholar 

  • Kumari K, Muthamilarasan M, Misra G, Gupta S, Subramanian A, Parida SK, Chattopadhyay D, Prasad M (2013) Development of eSSR-Markers in Setaria italica 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

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Li P, Brutnell TP (2011) Setaria viridis and Setaria italica, model genetic systems for the panicoid grasses. J Exp Bot 62:3031–3037

    Article  CAS  PubMed  Google Scholar 

  • 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

    Article  Google Scholar 

  • 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

    Google Scholar 

  • Liu K, Muse SV (2005) Powermarker: an integrated analysis environment for genetic marker data. Bioinformatics 21:2128–2129

    Article  CAS  PubMed  Google Scholar 

  • 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

    Google Scholar 

  • 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

    Article  Google Scholar 

  • 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

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • 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

    Article  Google Scholar 

  • 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

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • 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

    Article  CAS  Google Scholar 

  • 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

    PubMed Central  PubMed  Google Scholar 

  • Nei M (1972) Genetic distance between populations. Am Nat 106:283–392

    Article  Google Scholar 

  • Nei M (1973) Analysis of gene diversity in subdivided populations. PNAS 70:3321–3323

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • 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

    Article  Google Scholar 

  • 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

    Article  CAS  PubMed  Google Scholar 

  • 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

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Peakall R, Smouse PE (2006) GENALEX 6: genetic analysis in Excel. Population genetic software for teaching and research. Mol Ecol Notes 6(1):288–295

    Article  Google Scholar 

  • 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

    Article  PubMed  Google Scholar 

  • 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

    PubMed  Google Scholar 

  • Perrier X and Jacquemoud-Collet JP (2006) DARwin software (2006) http://darwin.cirad.fr/darwin

  • 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

    Article  Google Scholar 

  • Pritchard JK, Stephens M, Rosenberg NA, Donnelly P (2000a) Association mapping in structured populations. Am J Hum Genet 67:170–181

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Pritchard JK, Stephens M, Donnelly P (2000b) Inference of population structure using multilocus genotype data. Genetics 155:945–959

    CAS  PubMed Central  PubMed  Google Scholar 

  • 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

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • 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

    Article  CAS  Google Scholar 

  • 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

    Article  PubMed  Google Scholar 

  • 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

    Article  CAS  Google Scholar 

  • 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

    Article  Google Scholar 

  • 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

    Article  Google Scholar 

  • 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

    Article  CAS  PubMed  Google Scholar 

  • 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

    Article  CAS  Google Scholar 

  • 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

    Article  Google Scholar 

  • 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

    Article  CAS  PubMed  Google Scholar 

  • 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

    Article  PubMed Central  PubMed  Google Scholar 

  • 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 [Setaria italica (L.) Beauv.] landraces. Gene Genome Genet 2:769–777

    CAS  Google Scholar 

  • 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

    Article  PubMed  Google Scholar 

  • Whitt SR, Buckler ES (2003) Using natural allelic diversity to evaluate gene function. Methods Mol Biol 236:123–139

    CAS  PubMed  Google Scholar 

  • 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

    Article  PubMed  Google Scholar 

  • Yu J, Buckler ES (2006) Genetic association mapping and genome organization of maize. Curr Opin Biotech 17:155–160

    Article  CAS  PubMed  Google Scholar 

  • 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

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • 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

    Article  CAS  Google Scholar 

  • 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

    Article  PubMed Central  PubMed  Google Scholar 

  • Zhu CS, Gore M, Buckler ES, Yu JM (2008) Status and prospects of association mapping in plants. Plant Genome 1:5–20

    Article  CAS  Google Scholar 

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Acknowledgments

The authors gratefully acknowledge the financial support of the BMZ/GTZ project on “Sustainable conservation and utilization of genetic resources of two underutilized crops-finger millet and foxtail millet- to enhance productivity, nutrition and income in Africa and Asia” funded by the Federal Ministry for Economic Cooperation and Development (BMZ), Germany to carry out this activity.

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  1. S. Senthilvel

    Present address: Directorate of Oilseeds Research (DOR), Rajendranagar, Hyderabad, 500 030, Andhra Pradesh, India

Authors and Affiliations

  1. International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, 502 324, Andhra Pradesh, India

    M. Vetriventhan, Hari D. Upadhyaya, S. Senthilvel & R. K. Varshney

  2. Agricultural College and Research Institute, Tamil Nadu Agricultural University (TNAU), Madurai, 625 104, Tamil Nadu, India

    C. R. Anandakumar

  3. Institute of Plant Breeding, Seed Science and Population Genetics, University of Hohenheim, Fruwirthstr. 21, 70599, Stuttgart, Germany

    Heiko K. Parzies

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  1. M. Vetriventhan
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Correspondence to Hari D. Upadhyaya.

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Vetriventhan, M., Upadhyaya, H.D., Anandakumar, C.R. et al. Population structure and linkage disequilibrium of ICRISAT foxtail millet (Setaria italica (L.) P. Beauv.) core collection. Euphytica 196, 423–435 (2014). https://doi.org/10.1007/s10681-013-1044-6

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