Diversity and selection in sorghum: Simultaneous analyses using simple sequence repeats

Theoretical and Applied Genetics

Volumn 111, Issue 1, 2005, Pages 23-30

  Casa, A M ^a   Mitchell, S E ^a   Hamblin, M T ^a   Sun, H ^a   Bowers, J E ^b   Paterson, A H ^b   Aquadro, C F ^a   Kresovich, S ^a  

^a Department of Molecular Biology and Genetics   (United States)

^b UNIVERSITY OF GEORGIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BIOMARKERS; CULTIVATION; DNA; GENES; STATISTICAL METHODS;

GENE FLOW; LANDRACES; MOLECULAR MARKERS; SIMPLE SEQUENCE REPEAT (SSR);

CROPS;

ARTICLE; CLUSTER ANALYSIS; COMPARATIVE STUDY; GENETIC SELECTION; GENETIC VARIABILITY; GENETICS; POPULATION GENETICS; SORGHUM; VARIABLE NUMBER OF TANDEM REPEAT;

CLUSTER ANALYSIS; GENETICS, POPULATION; MINISATELLITE REPEATS; SELECTION (GENETICS); SORGHUM; VARIATION (GENETICS);

ALLELES; CULTIVATION; FARM CROPS; GENES; NUCLEIC ACIDS; SORGHUM; STATISTICAL ANALYSIS;

SORGHUM BICOLOR;

EID: 21444432552     PISSN: 00405752     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00122-005-1952-5     Document Type: Article

References (50)

1. Akey JM, Zhang G, Zhang K, Jin L, Shriver MD (2002) Interrogating a high-density SNP map for signatures of natural selection. Genome Res 12:1805-1814
2. Balloux F, Goudet J (2002) Statistical properties of population differentiation estimators under stepwise mutation in a finite island model. Mol Ecol 11:771-783
3. Beaumont MA, Nichols RA (1996) Evaluating loci for use in the genetic analysis of population structure. Proc R Soc London Ser B 263:1619-1626
4. Bhattramakki D, Dong J, Chhabra AK, Hart G (2000) An integrated SSR and RFLP linkage map of Sorghum bicolor (L.) Moench. Genome 43:988-1002
5. Bowers JE, Abbey C, Anderson S, Chang C, Draye X, Hoppe AH, Jessup R, Lemke C, Lennington J, Li Z, Lin YR, Liu SC, Luo L, Marler BS, Ming R, Mitchell SE, Qiang D, Reischmann K, Schulze SR, Skinner DN, Wang YW, Kresovich S, Schertz KF, Paterson AH (2003) A high-density genetic recombination map of sequence-tagged sites for sorghum, as a framework for comparative structural and evolutionary genomics of tropical grains and grasses. Genetics 165:367-386
6. Brown SM, Hopkins MS, Mitchell SE, Wang TY, Kresovich S, Duncan RR, Senior ML, Gonzales-Candelas F (1996) Multiple methods for the identification of polymorphic simple sequence repeats in sorghum [Sorghum bicolor (L.) Moench]. Theor Appl Genet 93:190-198
7. Chittenden LM, Schertz KF, Lin YR, Wing RA, Paterson AH (1994) A detailed RFLP map of Sorghum bicolor x S. propinquum, suitable for high-density mapping, suggests ancestral duplication of sorghum chromosomes or chromosomal segments. Theor Appl Genet 87:925-933
8. Cornuet JM, Luikart G (1996) Description and power analysis of two tests for detecting recent population bottlenecks from allele frequency data. Genetics 144:2001-2014
9. De Wet JMJ (1978) Systematics and evolution of Sorghum Sect. Sorghum (Gramineae). Am J Bot 65:477-484
10. Dean RE, Dahlberg JA, Hopkins MS, Mitchell SE, Kresovich S (1999) Genetic redundancy and diversity among Orange' accessions in the US National Sorghum Collection as assessed with simple sequence repeat (SSR) markers. Crop Sci 39:1215-1221
11. Di Rienzo A, Peterson AC, Garza JC, Valdes AM, Slatkin M, Freimer NB (1994) Mutational processes of simple-sequence repeat loci in human populations. Proc Natl Acad Sci USA 91:3166-3170
12. Dje Y, Heuertz M, Lefebvre C, Vekemans X (2000) Assessment of genetic diversity within and among germplasm accessions in cultivated sorghum using microsatellite markers. Theor Appl Genet 100:918-925
13. Doyle JJ, Doyle JL (1987) A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochem Bull 19:11-15
14. Efron B (1979) Bootstrap methods: another look at the jackknife. Ann Stat 7:1-26
15. FAO (2004) Production yearbook 2002 no. 56. FAO Statistic Series no. 176, Rome
16. 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
17. Goudet J (2001) FSTAT, a program to estimate and test gene diversities and fixation indices (version 2.9.3). Available from http://www.unil.ch/izea/ softwares/fstat.html
18. Grenier C, Bramel-Cox PJ, Noirot M, Prasada Rao KA, Hamon P (2000a) Assessment of genetic diversity in three subsets constituted from the ICRISAT sorghum collection using random vs. non-random sampling procedures. A. Using morpho-agronomical and passport data. Theor Appl Genet 101:190-196
19. Grenier C, Deu M, Kresovich S, Bramel-Cox PJ, Hamon P (2000b) Assessment of genetic diversity in three subsets constituted from the ICRISAT sorghum collection using random vs. non-random sampling procedures. B. Using molecular markers. Theor Appl Genet 101:197-202
20. Grenier C, Bramel-Cox PJ, Harmon P (2001) Core collection of sorghum: I. stratification based on eco-geographical data. Crop Sci 41:234-240
21. Hamblin MT, Mitchell SE, White GM, Gallego J, Kukatla R, Wing RA, Paterson AH, Kresovich S (2004) Comparative population genetics of the panicoid grasses: sequence polymorphism, linkage disequilibrium and selection in a diverse sample of Sorghum bicolor. Genetics 167:471-483
22. Harlan JR, De Wet JMJ (1972) A simplified classification of cultivated sorghum. Crop Sci 12:172-176
23. Harr B, Kauer M, Schlotterer C (2002) Hitchhiking mapping: a population-based fine-mapping strategy for adaptive mutations in Drosophila melanogaster. Proc Natl Acad Sci USA 99:12949-12954
24. Hu FY, Tao DY, Sacks E, Xu P, Li L, Yang Y, McNally K, Khush GS, Paterson AH, Li ZK (2003) Convergent evolution of perenniality in grasses. Proc Natl Acad Sci USA 100: 4050-4054
25. Kauer MO, Dieringer D, Schlotterer C (2003) A microsatellite variability screen for positive selection associated with the "out of Africa" habitat expansion of Drosophila melanogaster. Genetics 165:1137-1148
26. Kayser M, Brauer S, Stoneking M (2003) A genome scan to detect candidate regions influenced by local natural selection in human populations. Mol Biol Evol 20:893-900
27. Kimura M, Crow J (1964) The number of alleles that can be maintained in a finite population. Genetics 49:725-738
28. Kimura M, Ohta T (1978) Stepwise mutation model and distribution of allelic frequencies in a finite population. Proc Natl Acad Sci USA 75:2868-2872
29. Kong L, Dong J, Hart G (2000) Characteristics, linkage-map positions, and allelic differentiation of Sorghum bicolor (L.) Moench DNA simple sequence repeats (SSRs). Theor Appl Genet 101:438-448
30. Liu K, Muse S (2002) POWERMARKER: new genetic data analysis software (version. 3.0). Available from http://www.power-marker.net/
31. Matsuoka Y, Mitchell SE, Kresovich S, Goodman M, Doebley J (2002) Microsatellites in Zea-variability, patterns of mutations, and use for evolutionary studies. Theor Appl Genet 104:436-450
32. Maynard Smith J, Haigh J (1974) The hitchhiking effect of a favourable gene. Genet Res 23:23-35
33. 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
34. Nei M, Tajima F, Tateno Y (1983) Accuracy of estimated phylogenetic trees from molecular data. II. Gene frequency data. J Mol Evol 91:153-170
35. Paterson AH, Lin YR, Li Z, Schertz KF, Doebley JF, Pinson SRM, Liu SC, Stansel JW, Irvine JE (1995a) Convergent domestication of cereal crops by independent mutations at corresponding genetic loci. Science 269: 1714-1718
36. Paterson AH, Schertz KF, Lin YR, Liu SC, Chang YL (1995b) The weediness of wild plants: molecular analysis of genes responsible for dispersal and persistence of johnsongrass (Sorghum halepense L. Pers.). Proc Natl Acad Sci USA 92: 6127-6131
37. Payseur BA, Cutter AD, Nachman MW (2002) Searching for evidence of positive selection in the human genome using patterns of microsatellite variability. Mol Biol Evol 19:1143-1153
38. 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
39. Saitou N, Nei M (1987) The neighbor-joining method - a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406-425
40. Schloss SJ, Mitchell SE, White GM, Kukatla R, Bowers JE, Paterson AH, Kresovich S (2002) Characterization of RFLP probe sequences for gene discovery and SSR development in Sorghum bicolor (L.) Moench. Theor Appl Genet 105:912-920
41. Schlotterer C (2002) A microsatellite-based multilocus screen for the identification of local selective sweeps. Genetics 160:753-763
42. 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
43. 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). Proc Natl Acad Sci USA 98:9161-9166
44. 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
45. Vigouroux Y, McMullen M, Hittinger CT, Houchins K, Schulz L, Kresovich S, Matsuoka Y, Doebley J (2002) Identifying genes of agronomic importance in maize by screening microsatellites for evidence of selection during domestication. Proc Natl Acad Sci USA 99:9650-9655
46. Vigouroux Y, Mitchell SE, Matsuoka Y, Hamblin MT, Kresovich S, Smith JSC, Jaqueth J, Smith OS, Doebley J (2005) An analysis of genetic diversity across the maize genome using microsatellites. Genetics (in press)
47. Watterson GA (1978) The homozygosity test of neutrality. Genetics 88:405-417
48. Weir BS, Cockeram CC (1984) Estimating F-statistics for the analysis of population structure. Evolution 38: 1358-1370
49. Wright S (1949) Adaptation and selection. In: Jepson GL, Simpson GG, Mayr E (eds) Genetics, paleontology, and evolution. Princeton University Press, New Jersey, pp 365-389
50. Wright S (1951) The genetical structure of populations. Ann Eugenics 15:323-354