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Assessment of genetic diversity in the sorghum reference set using EST-SSR markers

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Abstract

Selection and use of genetically diverse genotypes are key factors in any crop breeding program to develop cultivars with a broad genetic base. Molecular markers play a major role in selecting diverse genotypes. In the present study, a reference set representing a wide range of sorghum genetic diversity was screened with 40 EST-SSR markers to validate both the use of these markers for genetic structure analyses and the population structure of this set. Grouping of accessions is identical in distance-based and model-based clustering methods. Genotypes were grouped primarily based on race within the geographic origins. Accessions derived from the African continent contributed 88.6 % of alleles confirming the African origin of sorghum. In total, 360 alleles were detected in the reference set with an average of 9 alleles per marker. The average PIC value was 0.5230 with a range of 0.1379–0.9483. Sub-race, guinea margaritiferum (Gma) from West Africa formed a separate cluster in close proximity to wild accessions suggesting that the Gma group represents an independent domestication event. Guineas from India and Western Africa formed two distinct clusters. Accessions belongs to the kafir race formed the most homogeneous group as observed in earlier studies. This analysis suggests that the EST-SSR markers used in the present study have greater discriminating power than the genomic SSRs. Genetic variance within the subpopulations was very high (71.7 %) suggesting that the germplasm lines included in the set are more diverse. Thus, this reference set representing the global germplasm is an ideal material for the breeding community, serving as a community resource for trait-specific allele mining as well as genome-wide association mapping.

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References

  • Abdurakhmonov IY, Abdukarimov A (2008) Application of association mapping to understand the genetic diversity of plant germplasm resources. Int J Plant Genomics. doi:10.1155/2008/574927

    PubMed  Google Scholar 

  • Agrama HA, Tuinstra MR (2003) Phylogenetic diversity and relationships among sorghum accessions using SSRs and RAPDs. Afr J Biotechnol 10:334–340

    Google Scholar 

  • Akimoto M, Shimamoto Y, Morishima H (1999) The extinction of genetic resources of Asian wild rice, Oryza rufipogon Griff.: a case study in Thailand. Genet Resour Crop Evol 46:419–425

    Article  Google Scholar 

  • Aldrich PR, Doebley J, Schertz KF, Stec A (1992) Patterns of allozyme variation in cultivated and wild Sorghum bicolor. Theor Appl Genet 85:451–460

    Article  CAS  Google Scholar 

  • Ali ML, Rajewski JF, Baenziger PS, Gill KS, Eskridge KM, Dweikat L (2008) Assessment of genetic diversity and relationship among a collection of US sweet sorghum germplasm by SSR markers. Mol Breed 21:497–509

    Article  CAS  Google Scholar 

  • Balyan HS, Gupta PK, Rustgi S, Bandopadhyay R, Goyal A, Singh R, Kumar A, Kumar N, Sharma S (2005) Development and use of SSRs of bread wheat for genetic and physical mapping and transferability to the species of Triticum–Aegilops complex. Czech J Genet Plant Breed 41:141–144

    Google Scholar 

  • Barnaud A, Deu M, Garine E, McKey D, Joly H (2007) Local genetic diversity of sorghum in a village in northern Cameroon: structure and dynamics of landraces. Theor Appl Genet 114:237–248

    Article  PubMed  Google Scholar 

  • Barro-Kondombo Sagnard F, Chantereau J, Deu M, Brocke KV, Durand P, Goze E, Zongo JD (2010) Genetic structure among sorghum landraces as revealed by morphological variation and microsatellite markers in three agroclimatic regions of Burkina Faso. Theor Appl Genet 120:1511–1523

    Article  CAS  PubMed  Google Scholar 

  • Bhattramakki D, Dong JM, Chhabra AK, Hart GE (2000) An integrated SSR and RFLP linkage map of Sorghum bicolor (L) Moench. Genome 43:988–1002

    CAS  PubMed  Google Scholar 

  • Billot C, Rivallan R, Sall MN, Fonceka D, Deu M, Glaszmann JC, Noyer JL, Rami JK, Risterucci AM, Wincker P, Ramu P, Hash CT (2012) A reference microsatellite kit to assess for genetic diversity of Sorghum bicolor (Poaceae). Am J Bot 6:e245–e260

    Article  Google Scholar 

  • Billot C, Ramu P, Bouchet S, Chantereau J, Deu M, Gardes L, Noyer JL, Rami JF, Rivallan R, Li Y, Lu P, Wang T, Folkertsma RT, Arnaud E, Upadhyaya HD, Glaszmann JC, Hash CT (2013) Massive sorghum collection genotyped with SSR markers to enhance use of global genetic resources. PLoS ONE 8(4):e59714. doi:10.1371/journal.pone.0059714

  • Bouchet S, Pot D, Deu M, Rami J-F, Billot C, Perrier X, Rivallan R, Gardes L, Xia L, Wenzl P, Kilian A, Glaszmann J-C (2012) Genetic structure, linkage disequilibrium and signature of selection in sorghum: lessons from physically anchored DArT markers. PLoS One 7(3):e33470. doi:10.1371/journal.pone.0033470

    Article  CAS  PubMed  Google Scholar 

  • Brown SM, Hopkins MS, Mitchell SE, Senior ML, Wang TY, Duncan RR, Gonzalez-Candelas F, Kresovich S (1996) Multiple methods for the identification of polymorphic simple sequence repeats (SSRs) in sorghum [Sorghum bicolor (L.) Moench]. Theor Appl Genet 93:190–198

    Article  CAS  Google Scholar 

  • Caniato FF, Guimarães CT, Schaffert RE, Alves VM, Kochian LV, Borem A, Klein PE, Magalhaes JV (2007) Genetic diversity for aluminum tolerance in sorghum. Theor Appl Genet 114:863–876

    Article  CAS  PubMed  Google Scholar 

  • Casa AM, Mitchell SE, Hamblin MT, Sun H, Bowers JE, Paterson AH, Aquadro CF, Kresovich S (2005) Diversity and selection in sorghum: simultaneous analyses using simple sequence repeats. Theor Appl Genet 111:23–30

    Article  CAS  PubMed  Google Scholar 

  • Casa AM, Pressoir G, Brown PJ, Mitchell SE, Rooney WL, Tuinstra MR, Franks CD, Kresovich S (2008) Community resources and strategies for association mapping in sorghum. Crop Sci 48:30–40

    Article  Google Scholar 

  • Cho YG, Ishii T, Temnykh S, Chen X, Lipovich L, McCouch SR, Park WD, Ayres N, Cartinhour S (2000) Diversity of microsatellites derived from genomic libraries and GenBank sequences in rice (Oryza sativa L.). Theor Appl Genet 100:713–722

    Article  CAS  Google Scholar 

  • Cui YX, Xu GW, Magill CW, Schertz KF, Hart GE (1995) RFLP-based assay of Sorghum bicolor (L) Moench genetic diversity. Theor Appl Genet 90:787–796

    Article  CAS  Google Scholar 

  • da Silva J, Solis-Gracia N (2006) Development of simple sequence repeat markers from genes related to stress resistance in sugarcane. Subtrop Plant Sci 58:5–11

    Google Scholar 

  • de Oliveira AC, Richter T, Bennetzen JL (1996) Regional and racial specificities in sorghum germplasm assessed with DNA markers. Genome 39:579–587

    Article  PubMed  Google Scholar 

  • Deu M, Gonzalez-de-Leon D, Glaszmann J-C, Degremont I, Chantereau J, Lanaud C, Hamon P (1994) RFLP diversity in cultivated sorghum in relation to racial differentiation. Theor Appl Genet 88:838–844

    Article  CAS  Google Scholar 

  • Deu M, Hamon P, Chantereau J, Dufour P, D’Hont A, Lanaud C (1995) Mitochondrial DNA diversity in wild and cultivated sorghum. Genome 38:635–645

    Article  CAS  PubMed  Google Scholar 

  • Deu M, Rattunde F, Chantereau J (2006) A global view of genetic diversity in cultivated sorghums using a core collection. Genome 49:168–180

    CAS  PubMed  Google Scholar 

  • Deu M, Sagnard F, Chantereau J, Calatayud C, Hérault D, Mariac C, Pham J-L, Vigouroux Y, Kapran I, Traore PS, Mamadou A, Gerard B, Ndjeunga J, Bezancon G (2008) Niger-wide assessment of in situ sorghum genetic diversity with microsatellite markers. Theor Appl Genet 116:903–913

    Article  CAS  PubMed  Google Scholar 

  • Deu M, Sagnard F, Chantereau J, Calatayud C, Vigouroux Y, Pham JL, Mariac C, Kapran I, Mamadou A, Gerard B, Ndjeunga J, Bezancon G (2010) Spatio-temporal dynamics of genetic diversity in Sorghum bicolor in Niger. Theor Appl Genet 120:1301–1313

    Article  PubMed  Google Scholar 

  • Dje` Y, Forcioli D, Ater M, Lefe`bvre C, Vekemans X (1999) Assessing population genetic structure of sorghum landraces from north-western Morocco using allozyme and microsatellite markers. Theor Appl Genet 99:157–163

    Article  Google Scholar 

  • Dje` Y, Heuertz M, Lefe`bvre C, Vekemans X (2000) Assessment of genetic diversity within and among germplasm accessions in 408 cultivated sorghum using microsatellite markers. Theor Appl Genet 100:918–925

    Article  CAS  Google Scholar 

  • Doggett H (1988) Sorghum, 2nd edn. Longman Scientific and Technical, London

    Google Scholar 

  • Ellis JR, Burke JM (2007) EST-SSRs as a resource for population genetic analyses. Heredity 99:125–132

    Article  CAS  PubMed  Google Scholar 

  • Eujayl I, Sorrells ME, Wolters P, Baum M, Powell W (2002) Isolation of EST-derived microsatellite markers for genotyping the A and B genomes of wheat. Theor Appl Genet 104:399–407

    Article  CAS  PubMed  Google Scholar 

  • Excoffier L, Laval G, Schneider S (2005) Arlequin ver. 3.0: an integrated software package for population genetics data analysis. Evol Bioinform Online 1:47–50

    CAS  Google Scholar 

  • Falush D, Stephens M, Pritchard JK (2003) Inference of population structure using multilocus genotyping data: linked loci and correlated allele frequencies. Genetics 164:1565–1587

    Google Scholar 

  • Folkertsma RT, Rattunde FH, Chandra S, Soma Raju W, Hash CT (2005) The pattern of genetic diversity of guinea-race Sorghum bicolor (L.) Moench landraces as revealed with SSR markers. Theor Appl Genet 111:399–409

    Article  CAS  PubMed  Google Scholar 

  • Ghebru B, Schmidt RJ, Bennetzen JL (2002) Genetic diversity of Eritrean sorghum landraces assessed with simple sequence repeat (SSR) markers. Theor Appl Genet 105:229–236

    Article  CAS  PubMed  Google Scholar 

  • Gupta PK, Rustgi S, Sharma S, Singh R, Kumar N, Balyan HS (2003) Transferable EST-SSR markers for the study of polymorphism and genetic diversity in bread wheat. Mol Genet Genomics 270:315–323

    Article  CAS  PubMed  Google Scholar 

  • Harlan JR (1992) Crops and man. ASA, Madison

    Google Scholar 

  • Jayashree B, Ramu P, Prasad P, Kassahun B, Hash CT, Chandra S, Hoisington DA, Varshney RK (2006) A database of simple sequence repeats from cereal and legume expressed sequence tags mined in silico: survey and evaluation. In Silico Biol 6:0054 (http://www.bioinfo.de/isb/2006/06/0054/)

  • Ji GS, Song YF, Liu GQ, Du RH, Hao FW (2011) Genetic analysis of sorghum resources from China using SSRs. J SAT Agric Res 9 (http://ejournal.icrisat.org/Volume9/Sorghum_Millets/Genetic_analysis_Ji.pdf)

  • Kantety RV, Rota ML, Matthews DE, Sorrells ME (2002) Data mining for simple sequence repeats in expressed sequence tags from barley, maize, rice, sorghum and wheat. Plant Mol Biol 48:501–510

    Article  CAS  PubMed  Google Scholar 

  • Kimura M, Crow JF (1964) The numbers of alleles that can be maintained in a finite population. Genetics 49:725–738

    CAS  PubMed  Google Scholar 

  • Kong L, Dong J, Hart GE (2000) Characteristics, linkage-map positions, and allelic differentiation of Sorghum bicolour (L.) Moench DNA simple-sequence repeats (SSRs). Theor Appl Genet 101:438–448

    Article  CAS  Google Scholar 

  • Leigh F, Lea V, Law J, Wolters P, Powell W, Donini P (2003) Assessment of EST- and genomic microsatellite markers for variety discrimination and genetic diversity studies in wheat. Euphytica 133:359–366

    Article  CAS  Google Scholar 

  • Li M, Yuyama N, Luo L, Hirata M, Cai H (2009) In silico mapping of 1758 new SSR markers developed from public genomic sequences for sorghum. Mol Breed 24:41–47

    Article  Google Scholar 

  • Liu K, Muse SV (2005) Powermarker: integrated analysis environment for genetic markers data. Bioinformatics 21(9):2128–2129

    Article  CAS  PubMed  Google Scholar 

  • Mace ES, Buhariwalla HK, Crouch JH (2003) A high throughput DNA extraction protocol for molecular breeding programs. Plant Mol Biol Rep 21:459a–459h

    Article  Google Scholar 

  • Mace ES, Xia L, Jordan DR, Halloran K, Parh DK, Huttner E, Wenzl P, Kilian A (2008) Dart markers: diversity analysis and mapping in Sorghum bicolor. BMC Genomics 9:26. doi:10.1186/1471-2164-9-26

    Article  PubMed  Google Scholar 

  • Mariac C, Robert T, Allinne C, Remigereau MS, Luxereau A, Tidjani M, Seyni O, Bezancon G, Pham JL, Sarr A (2006) Genetic diversity and gene flow among pearl millet crop/weed complex: a case study. Theor Appl Genet 113:1003–1014

    Article  CAS  PubMed  Google Scholar 

  • Menkir A, Goldsbrough P, Ejeta G (1997) RAPD based assessment of genetic diversity in cultivated races of sorghum. Crop Sci 37:564–569

    Article  CAS  Google Scholar 

  • Menz MA, Klein RR, Unruh NC, Rooney WL, Klein PE, Mullet JE (2004) Genetic diversity of public inbreds of sorghum determined by mapped AFLP and SSR markers. Crop Sci 44:1236–1244

    Article  CAS  Google Scholar 

  • Mian MAR, Saha MC, Hopkins AA, Wang Z-Y (2005) Use of tall fescue EST-SSR markers in phylogenetic analysis of cool-season forage grasses. Genome 48:637–647

    Article  CAS  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 

  • Ng’uni D, Geleta M, Bryngelsson T (2011) Genetic diversity in sorghum (Sorghum bicolor (L.) Moench) accessions of Zambia as revealed by simple sequence repeats (SSR). Hereditas 148:52–62

    Article  PubMed  Google Scholar 

  • Ngugi K, Onyango CM (2012) Analysis of the molecular diversity of Kenyan sorghum germplasm using microsatellites. J Crop Sci and Biotech 15:189–194

    Article  Google Scholar 

  • Ohta T, Kimura M (1973) A model of mutation appropriate to estimate the number of electrophoretically detectable alleles in a finite population. Genet Res 22:201–204

    Article  Google Scholar 

  • 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

    Article  CAS  PubMed  Google Scholar 

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

  • Perrier X, Flori A, Bonnot F (2003) Methods for data analysis. In: Hamon P, Seguin M, Perrier X, Glaszmann JC (eds) Genetic diversity of cultivated tropical plants. Science Publishers, Inc. and CIRAD, Montpellier, pp 31–63

    Google Scholar 

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

    CAS  PubMed  Google Scholar 

  • Ramu P, Kassahun B, Senthilvel S, Kumar CA, Jayashree B, Folkertsma RT, Reddy LA, Kuruvinashetti MS, Haussmann BIG, Hash CT (2009) Exploiting rice–sorghum synteny for targeted development of EST-SSRs to enrich the sorghum genetic linkage map. Theor Appl Genet 119:1193–1204

    Article  CAS  PubMed  Google Scholar 

  • Sagnard F, Deu M, Dembe′le′ D, Leblois R, Toure′ L, Diakite′ M, Calatayud C, Vaksma M (2011) Genetic diversity, structure, gene flow and evolutionary relationships within the Sorghum bicolor wild–weedy–crop complex in a western African region. Theor Appl Genet 123:1231–1246

    Article  PubMed  Google Scholar 

  • Saha MC, Mian MAR, Eujayl I, Zwonitzer JC, Wang L, May GD (2004) Tall fescue EST-SSR markers with transferability across several grass species. Theor Appl Genet 109:783–791

    Article  PubMed  Google Scholar 

  • Schloss SJ, Mitchell SE, White GM, Kukatla R, Bowers JE, Paterson AH, Kresovich S (2002) Characterization of RFLP clone sequences for gene discovery and SSR development in Sorghum bicolor (L.) Moench. Theor Appl Genet 105:912–920

    Article  CAS  PubMed  Google Scholar 

  • Senthilvel S, Jayashree B, Mahalakshmi V, Kumar PS, Nakka S, Nepolean T, Hash CT (2008) Development and mapping of simple sequence repeat markers for pearl millet from data mining of expressed sequence tags. BMC Plant Biol 8:119

    Article  CAS  PubMed  Google Scholar 

  • Smith JSC, Kresovich S, Hopkins MS, Mitchell SE, Dean RE, Woodman WL, Lee M, Porter K (2000) Genetic diversity among elite sorghum inbred lines assessed with simple sequence repeats. Crop Sci 40:226–232

    Article  CAS  Google Scholar 

  • Snow AA, Pilson D, Rieseberg LH, Paulsen M, Pleskac N, Reagon MR, Wolf DE, Selbo SM (2003) A Bt transgene reduces herbivory and enhances fecundity in wild sunflowers. Ecol Appl 13:279–286

    Article  Google Scholar 

  • Srinivas G, Satish K, Murali Mohan S, Nagaraja Reddy R, Madhusudhana R, Balakrishna D, Venkatesh Bhat B, Howarth CJ, Seetharama N (2008) Development of genic-microsatellite markers for sorghum staygreen QTL using a comparative genomic approach with rice. Theor Appl Genet 117:283–296

    Article  CAS  PubMed  Google Scholar 

  • Srinivas G, Satish K, Madhusudhana R, Seetharama N (2009) Exploration and mapping of microsatellite markers from subtracted drought stress ESTs in Sorghum bicolor (L.) Moench. Theor Appl Genet 118:703–717

    Article  CAS  PubMed  Google Scholar 

  • Studer B, Asp T, Frei U, Hentrup S, Meally H et al (2008) Expressed sequence tag-derived microsatellite markers in perennial ryegrass (Lolium perenne L.). Mol Breed 21:533–548

    Article  CAS  Google Scholar 

  • Tao Y, Manners JM, Ludlow MM, Henzell RG (1993) DNA polymorphisms in grain sorghum (Sorghum bicolor (L.) Moench). Theor Appl Genet 86:679–688

    Article  CAS  Google Scholar 

  • Taramino G, Tarchini R, Ferrario S, Lee M, Pe′ ME (1997) Characterization and mapping of simple sequence repeats (SSRs) in Sorghum bicolor. Theor Appl Genet 95:66–72

    Article  CAS  Google Scholar 

  • Tesso T, Kapran I, Grenier C, Snow A, Sweeney P, Pedersen J, Marx D, Bothma G, Ejeta G (2008) The potential for crop-to-wild gene flow in sorghum in Ethiopia and Niger: a geographic survey. Crop Sci 48:1425–1431

    Article  Google Scholar 

  • Thiel T, Michalek W, Varshney RK, Graner A (2003) Exploiting EST databases for the development and characterization of gene-derived SSR-markers in barley (Hordeum vulgare L.). Theor Appl Genet 106:411–422

    CAS  PubMed  Google Scholar 

  • Upadhyaya HD, Wang Y-H, Sharma S, Singh S (2012) Association mapping of height and maturity across five environments using the sorghum mini core collection. Genome 55:471–479

    Article  CAS  PubMed  Google Scholar 

  • Uptmoor R, Wenzel W, Friedt W, Donaldson G, Ayisi K, Ordon F (2003) Comparative analysis on the genetic relatedness of Sorghum bicolor accessions from Southern Africa by RAPDs, AFLPs and SSRs. Theor Appl Genet 106:1316–1325

    CAS  PubMed  Google Scholar 

  • Varshney RK, Thiel T, Stein N, Langridge P, Graner A (2002) In silico analysis of frequency and distribution of microsatellites in ESTs of some cereal species. Cell Mol Biol Lett 7:537–546

    CAS  PubMed  Google Scholar 

  • Varshney RK, Grosse I, Hähnel U, Siefken R, Prasad M, Stein N, Langridge P, Altschmied L, Graner A (2006) Genetic mapping and BAC assignment of EST-derived SSR markers shows non-uniform distribution of genes in barley genome. Theor Appl Genet 113:239–250

    Article  CAS  PubMed  Google Scholar 

  • Varshney RK, Thiel T, Sretenovic-Rajicic T, Baum M, Valkoun J, Guo P, Grando S, Ceccarelli S, Graner A (2008) Identification and validation of a core set of informative genic SSR and SNP markers for assaying functional diversity in barley. Mol Breed 22:1–13

    Article  CAS  Google Scholar 

  • Wang ML, Barkley NA, Yu J-K, Dean RE, Newman ML, Sorrells ME, Pederson GA (2005) Transfer of simple sequence repeat (SSR) markers from major cereal crops to minor grass species for germplasm characterization and evaluation. Plant Genet Resour Charact Util 3:45–57

    Article  CAS  Google Scholar 

  • Wang ML, Mosjidis JA, Morris JB, Dean RE, Jenkins TM, Paderson GA (2006) Genetic diversity of Crotalaria germplasm assessed through phylogenetic analysis of EST-SSR markers. Genome 49:707–715

    Article  CAS  PubMed  Google Scholar 

  • Wang ML, Zhu C, Barkley NA, Chen Z, Erpelding JE, Murray SC, Tuinstra MR, Tesso T, Pederson GA, Yu J (2009) Genetic diversity and population structure analysis of accessions in the US historic sweet sorghum collection. Theor Appl Genet 120:13–23

    Article  PubMed  Google Scholar 

  • Yu J, Dake TM, Singh S, Benscher D, Li W, Gill B, Sorrells ME (2004) Development and mapping of EST-derived simple sequence repeat (SSR) markers for hexaploid wheat. Genome Res 47:805–818

    Article  CAS  Google Scholar 

  • Zhang LY, Ravel C, Bernard M, Balfourier F, Leroy P, Feuillet C, Sourdille P (2006) Transferable bread wheat EST-SSRs can be useful for phylogenetic studies among the Triticeae species. Theor Appl Genet 113:407–418

    Article  CAS  PubMed  Google Scholar 

  • Zheng L-Y, Guo X-S, He B, Sun L-J, Peng Y, Dong S–S, Liu T-F, Jiang S, Ramachandran R, Liu C-M, Jing H-C (2011) Genome-wide patterns of genetic variation in sweet and grain sorghum (Sorghum bicolor). Genome Biol 12:R114

    Article  CAS  PubMed  Google Scholar 

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

    Article  CAS  Google Scholar 

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Acknowledgments

We thank the two anonymous reviewers for their helpful suggestions and comments. This work is a part of the Ph.D. thesis of PR. The research fellowship provided to PR by the Council of Scientific and Industrial Research (CSIR), New Delhi, India is greatly acknowledged. Work reported here was supported by the grant from the Generation Challenge Programme (GCP) of the CGIAR.

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Authors and Affiliations

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

    P. Ramu, S. Senthilvel, H. D. Upadhyaya & C. T. Hash

  2. Department of Genetics, Osmania University, Hyderabad, 500 007, Andhra Pradesh, India

    P. Ramu & L. Ananda Reddy

  3. Cirad, UMR AGAP, 34398, Montpellier, France

    C. Billot & J-F. Rami

  4. ICRISAT Sahelian Center, 12404, Niamey, Niger

    C. T. Hash

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  1. P. Ramu
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  2. C. Billot
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  3. J-F. Rami
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  4. S. Senthilvel
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  5. H. D. Upadhyaya
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  6. L. Ananda Reddy
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Communicated by H.-C. Jing.

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Supplemental table S1: List of 384 accessions included in reference set of sorghum and their passport information.

Supplemental table S2: Data matrix of allele calls used in the present study for 384 accessions across 40 EST-SSR markers. Missing data points were scored as numerical “zero (0)″s.

Supplemental figure S3: Dendrogram of reference set without their wild relatives. Cluster analysis with (Fig. 2) and without (supplemental figure S3) wild accessions suggest that they have greater similarity in grouping patterns according to their races within geographic origins.

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Ramu, P., Billot, C., Rami, JF. et al. Assessment of genetic diversity in the sorghum reference set using EST-SSR markers. Theor Appl Genet 126, 2051–2064 (2013). https://doi.org/10.1007/s00122-013-2117-6

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