Genetic structure and linkage disequilibrium in a diverse, representative collection of the c4 model plant, sorghum bicolor

G3: Genes, Genomes, Genetics

Volumn 3, Issue 5, 2013, Pages 783-793

  Wang, Yi Hong ^a   Upadhyaya, Hari D ^b   Burrell, A Millie ^c   Sahraeian, Sayed Mohammad Ebrahim ^d   Klein, Robert R ^e   Klein, Patricia E ^c  

^a UNIVERSITY OF LOUISIANA AT LAFAYETTE   (United States)

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

^c TEXAS A AND M UNIVERSITY   (United States)

^d Texas AandM University   (United States)

^e SOUTHERN PLAINS AGRICULTURAL RESEARCH CENTER   (United States)

Author keywords

FseI assisted genotyping; Linkage disequilibrium; Races; SNPs; Sorghum

Indexed keywords

CARBON;

AFRICA; ARTICLE; BIOLOGICAL MODEL; CHROMOSOME 1; CHROMOSOME 10; CHROMOSOME 2; CHROMOSOME 9; CLUSTER ANALYSIS; DOMESTICATION; ECOTYPE; EUCHROMATIN; FSEI-ASSISTED GENOTYPING; GENE LINKAGE DISEQUILIBRIUM; GENE MAPPING; GENE SEQUENCE; GENETIC TRAIT; GENETIC VARIABILITY; GENETICS; GENOTYPE; GENOTYPING TECHNIQUE; GEOGRAPHIC DISTRIBUTION; GEOGRAPHIC ORIGIN; GUINEA; HETEROCHROMATIN; INDIA; LANDRACE; METABOLISM; NONHUMAN; PHYLOGENY; PLANT CHROMOSOME; PLANT GENE; POPULATION DYNAMICS; PRINCIPAL COMPONENT ANALYSIS; RACES; SELECTIVE SWEEP; SINGLE NUCLEOTIDE POLYMORPHISM; SNPS; SORGHUM;

SORGHUM BICOLOR;

EID: 84878365683     PISSN: None     EISSN: 21601836     Source Type: Journal    
DOI: 10.1534/g3.112.004861     Document Type: Article

References (67)

1. Altschul, S. F., T. L. Madden, A. A. Schäffer, J. Zhang, Z. Zhang et al., 1997 Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25: 3389-3402.
2. Baird, N. A., P. D. Etter, T. S. Atwood, M. C. Currey, A. L. Shiver, et al. 2008 Rapid SNP discovery and genetic mapping using sequenced RAD markers. PLoS ONE 3: e3376.
3. Becker, R. A, J. M. Chambers, and A. R. Wilks, 1988 The New S Language. Wadsworth & Brooks/Cole, Pacific Grove, PA.
4. Bergelson, J., and F. Roux, 2010 Towards identifying genes underlying ecologically relevant traits in Arabidopsis thaliana. Nat. Rev. Genet. 11: 867-879.
5. Bouchet, S., D. Pot, M. Deu, J.-F. Rami, C. Billot, et al. 2012 Genetic structure, linkage disequilibrium and signature of selection in sorghum: lessons from physically anchored DArT markers. PLoS ONE 7: e33470.
6. Bradbury, P. J., Z. Zhang, D. E. Kroon, T. M. Casstevens, Y. Ramdoss, et al. 2007 TASSEL: Software for association mapping of complex traits in diverse samples. Bioinformatics 23: 2633-2635.
7. Brown, P. J., S. Myles, and S. Kresovich, 2011 Genetic support for phenotype- based racial classification in sorghum. Crop Sci. 51: 224-230.
8. Casa, A. M., S. E. Mitchell, M. T. Hamblin, H. Sun, J. E. Bowers, et al. 2005 Diversity and selection in sorghum: Simultaneous analyses using simple sequence repeats. Theor. Appl. Genet. 111: 23-30.
9. Casa, A., G. Pressoir, P. Brown, S. Mitchell, W. Rooney, et al. 2008 Community resources and strategies for association mapping in sorghum. Crop Sci. 48: 30-40.
10. Cui, Y. X., G. W. Xu, C. W. Magill, K. F. Schertz, and G. E. Hart, 1995 RFLP-based assay of Sorghum bicolor (L.) Moench genetic diversity. Theor. Appl. Genet. 90: 787-796.
11. Dahlberg, J. A., X. Zhang, G. E. Hart, and J. E. Mullet, 2002 Comparative assessment of variation among sorghum germplasm accessions using seed morphology and RAPD measurements. Crop Sci. 42: 291-296.
12. Davey, J. W., and M. L. Blaxter, 2010 RADSeq: Next-generation population genetics. Brief. Funct. Genomics 9: 416-423.
13. de Oliveira, A. C., T. Richter, and J. L. Bennetzen, 1996 Regional and racial specificities in sorghum germplasm assessed with DNA markers. Genome 39: 579-587.
14. de Wet, J. M. J., 1978 Systematics and evolution of sorghum sect. Sorghum (Gramineae). Am. J. Bot. 65: 477-484.
15. de Wet, J. M. J., and J. P. Huckabay, 1967 The origin of Sorghum bicolor. II. Distribution and domestication. Evolution 21: 787-802.
16. Deu, M., D. Gonzalez-de-Leon, J. C. Glaszmann, I. Degremont, J. Chantereau, et al. 1994 RFLP diversity in cultivated sorghum in relation to racial differentiation. Theor. Appl. Genet. 88: 838-844.
17. Deu, M., F. Sagnard, J. Chantereau, C. Calatayud, D. Hérault, et al. 2008 Niger-wide assessment of in situ sorghum genetic diversity with microsatellite markers. Theor. Appl. Genet. 116: 903-913.
18. Dillon, S. L., F. M. Shapter, R. J. Henry, G. Cordeiro, L. Izquierdo, et al. 2007 Domestication to crop improvement: Genetic resources for Sorghum and Saccharum (Andropogoneae). Ann. Bot. (Lond.) 100: 975-989.
19. Djé, Y., M. Heuertz, C. Lefébvre, and X. Vekemans, 2000 Assessment of genetic diversity within and among germplasm accessions in cultivated sorghum using microsatellite markers. Theor. Appl. Genet. 100: 918-925.
20. Elshire, R. J., J. C. Glaubitz, Q. Sun, J. A. Poland, K. Kawamoto, et al. 2011 A robust, simple genotyping-by-sequencing (GBS) approach for high diversity species. PLoS ONE 6: e19379.
21. Fan, C., Y. Xing, H. Mao, T. Lu, B. Han, et al. 2006 GS3, a major QTL for grain length and weight and minor QTL for grain width and thickness in rice, encodes a putative transmembrane protein. Theor. Appl. Genet. 112: 1164-1171.
22. Folkertsma, R. T., H. F. W. Rattunde, S. Chandra, G. S. Raju, and C. T. Hash, 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.
23. Ghebru, B. G., R. S. Schmidt, and J. B. Bennetzen, 2002 Genetic diversity of Eritrean sorghum landraces assessed with simple sequence repeat (SSR) markers. Theor. Appl. Genet. 105: 229-236.
24. Gore, M. A., J.-M. Chia, R. J. Elshire, Q. Sun, E. S. Ersoz, et al. 2009 A firstgeneration haplotype map of maize. Science 326: 1115-1117.
25. Grenier, C., P. Hamon, and P. J. Bramel-Cox, 2001 Core collection of sorghum: II. Comparison of three random sampling strategies. Crop Sci. 41: 241-246.
26. Gupta, P., S. Rustgi, and P. Kulwal, 2005 Linkage disequilibrium and association studies in higher plants: Present status and future prospects. Plant Mol. Biol. 57: 461-485.
27. Hamblin, M. T., M. G. Salas Fernandez, A. M. Casa, S. E. Mitchell, A. H. Paterson, et al. 2005 Equilibrium processes cannot explain high levels of short- and medium-range linkage disequilibrium in the domesticated grass Sorghum bicolor. Genetics 171: 1247-1256.
28. Harlan, J. R., and J. M. J. de Wet, 1972 A simplified classification of cultivated sorghum. Crop Sci. 12: 172-176.
29. Huang, C.-L., C.-Y. Hung, Y.-C. Chiang, C.-C. Hwang, T.-W. Hsu, et al. 2012 Footprints of natural and artificial selection for photoperiod pathway genes in Oryza. Plant J. 70: 769-782.
30. Kardailsky, I., V. K. Shukla, J. H. Ahn, N. Dagenais, S. K. Christensen, et al. 1999 Activation tagging of the floral inducer FT. Science 286: 1962-1965.
31. Kim, J.-S., M. N. Islam-Faridi, P. E. Klein, D. M. Stelly, H. J. Price, et al. 2005 Comprehensive molecular cytogenetic analysis of sorghum genome architecture: Distribution of euchromatin, heterochromatin, genes and recombination in comparison to rice. Genetics 171: 1963-1976.
32. Kimber, C. T., 2000 Origins of domesticated sorghum and its early diffusion to India and China, pp. 3-98 in Sorghum, edited by C. W. Smith, and R. A. Frederiksen. John Wiley, New York.
33. Kobayashi, Y., H. Kaya, K. Goto, M. Iwabuchi, and T. Araki, 1999 A pair of related genes with antagonistic roles in mediating flowering signals. Science 286: 1960-1962.
34. Komatsuda, T., M. Pourkheirandish, C. He, P. Azhaguvel, H. Kanamori, et al. 2007 Six-rowed barley originated from a mutation in a homeodomainleucine zipper I-class homeobox gene. Proc. Natl. Acad. Sci. USA 104: 1424-1429.
35. Li, Q., X. Yang, G. Bai, M. Warburton, G. Mahuku, et al. 2010 Cloning and characterization of a putative GS3 ortholog involved in maize kernel development. Theor. Appl. Genet. 120: 753-763.
36. Lin, Z., X. Li, L. M. Shannon, C.-T. Yeh, M. L. Wang, et al. 2012 Parallel domestication of the shattering1 genes in cereals. Nat. Genet. 44: 720-724.
37. Lloyd, J. R., A. Blennow, K. Burhenne, and J. Kossmann, 2004 Repression of a novel isoform of disproportionating enzyme (stdpe2) in potato leads to inhibition of starch degradation in leaves but not tubers stored at low temperature. Plant Physiol. 134: 1347-1354.
38. Mace, E., and D. Jordan, 2011 Integrating sorghum whole genome sequence information with a compendium of sorghum QTL studies reveals uneven distribution of QTL and of gene-rich regions with significant implications for crop improvement. Theor. Appl. Genet. 123: 169-191.
39. Mace, E. S., L. Xia, D. R. Jordan, K. Halloran, D. K. Parh, et al. 2008 DArT markers: Diversity analyses and mapping in Sorghum bicolor. BMC Genomics 9: 10.1186/1471-2164-1189-1126.
40. Mann, J. A., C. T. Kimber, and F. R. Miller, 1983 The origin and early cultivation of sorghums in Africa. Bull B Texas Agric Exper Station 1454: 107-153.
41. Mather, K. A., A. L. Caicedo, N. R. Polato, K. M. Olsen, S. McCouch, et al. 2007 The extent of linkage disequilibrium in rice (Oryza sativa L.). Genetics 177: 2223-2232.
42. Menkir, A., P. Goldsbrough, and G. Ejeta, 1997 RAPD based assessment of genetic diversity in cultivated races of sorghum. Crop Sci. 37: 564-569.
43. Menz, M. A., R. R. Klein, N. C. Unruh, W. L. Rooney, P. E. Klein, et al. 2004 Genetic diversity of public inbreds of sorghum determined by mapped AFLP and SSR markers. Crop Sci. 44: 1236-1244.
44. Nelson, D. E., P. P. Repetti, T. R. Adams, R. A. Creelman, J. Wu, et al. 2007 Plant nuclear factor Y (NF-Y) B subunits confer drought tolerance and lead to improved corn yields on water-limited acres. Proc. Natl. Acad. Sci. USA 104: 16450-16455.
45. Nelson, J., S. Wang, Y. Wu, X. Li, G. Antony, et al. 2011 Single-nucleotide polymorphism discovery by high-throughput sequencing in sorghum. BMC Genomics 12: 352.
46. Nordborg, M., J. Borevitz, J. Bergelson,C. Berry, J. Chory, et al. 2002 The extent of linkage disequilibrium in Arabidopsis thaliana. Nat. Genet. 30: 190-193.
47. Palaisa, K. A., M. Morgante, M. Williams, and A. Rafalski, 2003 Contrasting effects of selection on sequence diversity and linkage disequilibrium at two phytoene synthase loci. Plant Cell 15: 1795- 1806.
48. Paterson, A. H., J. E. Bowers, R. Bruggmann, I. Dubchak, J. Grimwood, et al. 2009 The Sorghum bicolor genome and the diversification of grasses. Nature 457: 551-556.
49. Perumal, R., R. Krishnaramanujam, M. A. Menz, S. Katilé, J. Dahlberg, et al. 2007 Genetic diversity among sorghum races and working groups based on AFLPs and SSRs. Crop Sci. 47: 1375-1383.
50. Pritchard, J. K., M. Stephens, and P. Donnelly, 2000 Inference of population structure using multilocus genotype data. Genetics 155: 945-959.
51. Remington, D. L., J. M. Thornsberry, Y. Matsuoka, L. M. Wilson, S. R. Whitt, et al. 2001 Structure of linkage disequilibrium and phenotypic associations in the maize genome. Proc. Natl. Acad. Sci. USA 98: 11479- 11484.
52. Ripley, B. D., 2001 The R project in statistical computing. MSOR Connections. The newsletter of the LTSN Maths. Stats & OR Network 1: 23-25.
53. Ritter, K., C. Mcintyre, I. Godwin, D. Jordan, and S. Chapman, 2007 An assessment of the genetic relationship between sweet and grain sorghums, within Sorghum bicolor ssp. bicolor (L.) Moench, using AFLP markers. Euphytica 157: 161-176.
54. Sakuma, S., M. Pourkheirandish, T. Matsumoto, T. Koba, and T. Komatsuda, 2010 Duplication of a well-conserved homeodomain-leucine zipper transcription factor gene in barley generates a copy with more specific functions. Funct. Integr. Genomics 10: 123-133.
55. Scheet, P., and M. Stephens, 2006 A fast and flexible statistical model for large-scale population genotype data: Applications to inferring missing genotypes and haplotypic phase. Am. J. Hum. Genet. 78: 629-644.
56. Smith, C. W., 1995 Crop Production: Evolution, History, and Technology. John Wiley & Sons, New York.
57. Stemler, A. B. L., J. R. Harlan, and J. M. J. Dewet, 1975 Caudatum sorghums and speakers of Chari-Nile languages in Africa. J. Afr. Hist. 16: 161-183.
58. Takano-Kai, N., H. Jiang, T. Kubo, M. Sweeney, T. Matsumoto, et al. 2009 Evolutionary history of GS3, a gene conferring grain length in rice. Genetics 182: 1323-1334.
59. Tamaki, S., S. Matsuo, H. L. Wong, S. Yokoi, and K. Shimamoto, 2007 Hd3a protein is a mobile flowering signal in rice. Science 316: 1033-1036.
60. Tamura, K., and M. Nei, 1993 Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Mol. Biol. Evol. 10: 512-526.
61. Tamura, K., D. Peterson, N. Peterson, G. Stecher, M. Nei, et al. 2011 Mega5: Molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol. Biol. Evol. 28: 2731-2739.
62. Upadhyaya, H., Y.-H. Wang, S. Sharma, S. Singh, and K. Hasenstein, 2012 SSR markers linked to kernel weight and tiller number in sorghum identified by association mapping. Euphytica 187: 401-410.
63. Upadhyaya, H. D., R. P. S. Pundir, S. L. Dwivedi, C. L. L. Gowda, V. G. Reddy, et al. 2009 Developing a mini core collection of sorghum for diversified utilization of germplasm. Crop Sci. 49: 1769-1780.
64. Wang, Y.-H., D. D. Poudel, and K. H. Hasenstein, 2011 Identification of SSR markers associated with saccharification yield using pool-based genome- wide association mapping in sorghum. Genome 54: 883-889.
65. Wang, Y.-H., P. Bible, R. Loganantharaj, and H. Upadhyaya, 2012 Identification of SSR markers associated with height using pool-based genome-wide association mapping in sorghum. Mol. Breed. 30: 281-292.
66. Whipple, C. J., T. H. Kebrom, A. L. Weber, F. Yang, D. Hall, et al. 2011 Grassy tillers1 promotes apical dominance in maize and responds to shade signals in the grasses. Proc. Natl. Acad. Sci. USA 108: E506-E512.
67. Zeeman, S. C., J. Kossmann, and A. M. Smith, 2010 Starch: Its metabolism, evolution, and biotechnological modification in plants. Annu. Rev. Plant Biol. 61: 209-234.