Assessment of molecular diversity and population structure of the Ethiopian sorghum [Sorghum bicolor (L.) Moench] germplasm collection maintained by the USDA-ARS National Plant Germplasm System using SSR markers

Genetic Resources and Crop Evolution

Volumn 60, Issue 6, 2013, Pages 1817-1830

  Cuevas, Hugo E ^a   Prom, Louis K ^b  

^a AGRICULTURAL RESEARCH SERVICE   (United States)

^b SOUTHERN PLAINS AGRICULTURAL RESEARCH CENTER   (United States)

Author keywords

Ethiopia; Genetic diversity; Genetic redundancy; Population structure; Sorghum bicolor

Indexed keywords

GENETIC MARKER; GENETIC RESOURCE; GENETIC VARIATION; GERMPLASM; HETEROZYGOSITY; MOLECULAR ANALYSIS; PLANT BREEDING; POPULATION STRUCTURE; SORGHUM; SUBPOPULATION;

ETHIOPIA;

SORGHUM BICOLOR;

EID: 84882873490     PISSN: 09259864     EISSN: None     Source Type: Journal    
DOI: 10.1007/s10722-013-9956-5     Document Type: Article

References (61)

1. Abdi A, Bekele E, Asfaw Z, Teshome A (2002) Patterns of morphological variation of sorghum (Sorghum bicolor (L.) Moench) landraces in qualitative characters in North Shewa and South Welo, Ethiopia. Hereditas 137: 161-172.
2. Ali ML, Rajewski JF, Baenziger PS, Gill KS, Eskridge KM, Dweikat I (2008) Assessment of genetic diversity and relationship among a collection of US sweet sorghum germplasm by SSR markers. Mol Breeding 21: 497-509.
3. Ayana A, Bekele E (1998) Geographical patterns of morphological variation in Sorghum (Sorghum bicolor (L.) Moench) germplasm from Ethiopia and Eritrea: qualitative characters. Hereditas 129: 195-205.
4. Ayana A, Bekele E (1999) Multivariate analysis of morphological variation in sorghum (Sorghum bicolor (L.) Moench) germplasm from Ethiopia and Eritrea. Genet Resour Crop Evol 46: 273-284.
5. Ayana A, Bekele E, Bryngelsson T (2000) Genetic variation in wild sorghum (Sorghum bicolor ssp. verticilliflorum (L.) Moench) germplasm from Ethiopia assessed by random amplified polymorphic DNA (RAPD). Hereditas 132: 249-254.
6. Bhosale SU, Stich B, Rattunde HF, Weltzien E, Haussmann BIG, Hash CT, Melchinger AE, Parzies HK (2011) Population structure in sorghum accessions from West Africa differing in race and maturity class. Genetica 139: 453-463.
7. Bohasale SU, Stich B, Rattunde HF, Weltzien E, Haussmann BIG, Hash CT, Melchinger AE, Parzies HK (2011) Population structure in sorghum accessions from West Africa differing in race and maturity class. Genetica 139: 453-463.
8. Casa AM, Pressoir G, Brown P, 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.
9. Dahlberg J (2000) Classification and characterization of sorghum. In: Smith CW, Frederisken RA (eds) Sorghum. Wiley, New York, pp 99-130.
10. Degu E (1996) Sorghum breeding and achievements in Ethiopia. In: Deressa A, Seboka B (eds) Research achievements and technology transfer attempts: vignettes from Shoa. In: Proceedings from the first technology generation, transfer, and gap analysis workshop, 25-27 Dec 1995, Nazret, Ethiopia.
11. Deu M, Sagnard F, Chantereau J, Calatayud C, Hérault D, Mariac C, Pham JL, Vigouroux Y, Traore PS, Mamadou A, Gerard B, Ndjeunga J, Bezancon G (2008) Niger-wide assessment of in situ sorghum diversity with microsatellite markers. Theor Appl Genet 116: 903-913.
12. Djè Y, Heuertz M, Ater M, Lefèbvre C, Vekemans X (2004) In situ estimation of out crossing rate in sorghum landraces using microsatellite markers. Euphytica 138: 205-212.
13. Doggett H (1988) Sorghum, 2nd edn. Longman Scientific and Technical, London.
14. Earl DA, vonHoldt BM (2012) STRUCTURE HARVESTER: a website and program for visualizing STRUCTURE output and implementing the Evanno method. Conserv Genet Resour 4: 359-361.
15. Ejeta J, Grenier C (2005) Sorghum and its weedy hybrids. In: Gressel J (ed) Crop ferality and volunteerism. CRC Press, Boca Raton, pp 123-135.
16. Elshire RJ, Glaubitz JC, Qi S, Kawamoto K, Buckler ES, Mitchell SE (2011) A robust, simple genotyping by sequencing (GBS) approach for high diversity species. PLoS ONE 6(5): e19379. doi: 10. 1371/journal. pone. 0019379.
17. England PR, Cornuet JM, Berthier P, Tallmon DA, Luikart G (2006) Estimating effective population size from linkage disequilibrium: severe bias in small samples. Conserv Genet 7: 303-308.
18. Erpelding J (2009) Anthracnose diseases response for photoperiod-insensitive Ethiopian germplasm from the U. S. sorghum collection. World J Agric Sci 5: 707-713.
19. Erpelding J, Wang ML (2007) Response to anthracnose infection for a random selection of sorghum germplasm. Plant Pathol J 6: 127-133.
20. Evano G, Regnaut S, Goudet J (2005) Detecting the number of cluster of individuals using the software STRUCTURE: a simulation study. Mol Ecol 14: 2611-2620.
21. Excoffier L, Laval G, Schneider S (2005) Arlequin (version 3. 0): an integrated software package for population genetic analysis. Evol Bioinform Online 1: 47-50.
22. Food and Agriculture Organization of the United Nation (FAO) (2010) FAOSTAT. http://faostat. fao. org/site/339/default. aspx. Accessed April 2012.
23. Gebrekidan B (1973) The importance of the Ethiopian sorghum germplasm in the world sorghum collection. Econ Bot 27: 442-445.
24. Ghebru B, Schmidt RJ, Bebbetzen JL (2002) Genetic diversity sorghum landraces assessed with simple sequence repeat (SSR) markers. Theor Appl Genet 105: 229-236.
25. Grenier C, Bramel-Cox PJ, Hamon P (2001a) Core collection of sorghum: I. Stratification based on eco-geographical data. Crop Sci 41: 234-239.
26. Grenier C, Hamon P, Bramel-Cox PJ (2001b) Core collection of sorghum: II. Comparison of three random sampling strategies. Crop Sci 41: 241-246.
27. GRIN (2012) USDA-ARS National Genetic Resources Program, Germplasm Resource Information Network (GRIN). Online database. National Germplasm Resources Laboratory, Beltsville, MD, USA. http://www. ars-grin. gov/. Accessed May 2012.
28. Han Z, Jian-Cheng W, Dong-Jian W, Feng-Xia Y, Jin-Fang XU, Guo-An S, Yan-An G, Ru-Yu L (2011) Assessment of genetic diversity in Chinese sorghum landraces using SSR markers as compared with foreign accessions. Acta Agron Sin 37: 224-234.
29. Harlan JR (1992) Indigenous African agriculture. In: Cowman CW, Watson PJ (eds) The origins of agriculture: an international perspective. Smithsonian Institution Press, Washington, DC, pp 59-70.
30. Harlan JR, de Wet JMJ (1972) Simplified classification of cultivated sorghum. Crop Sci 12: 172-176.
31. Harlan JR, Stemler A (1976) The races of sorghum in Africa. In: Harlan JR, de Wet JMJ, Stemler A (eds) Origins of African plant domestication. Mouton, The Hague.
32. Hash CT, Ramu P, Upadhyaya HD, Folkertsma RT, Billot C, Rami J-F, Rivallan R, Deu M, Chantereau J, Gardes L, Li, Y, Wang T, Lu P (2008) Diversity analysis of sorghum global composite collection and reference set. Poster presented in generation challenge program (GCP) annual review meeting (ARM), 16-20 Sept 2008, Bangkok, Thailand. http://www. generationcp. org/UserFiles/File/2008_Poster-abstracts_final. pdf.
33. Hill WG (1981) Estimation of effective population size from data on linkage disequilibrium. Genet Res (Camb) 38: 209-216.
34. Jakobsson M, Rosenberg NA (2007) CLUMPP: a cluster matching and permutation program for dealing with label switching and multimodality in analysis of population structure. Bioinformatics 23: 1801-1806.
35. Letunic I, Bork P (2011) Interactive tree of life v2: online annotation and display of phylogenetic trees made easy. Nucleic Acids Res 39: 475-478.
36. Liu K, Muse SV (2005) PowerMarker: integrated analysis environment for genetic marker data. Bioinformatics 21: 2128-2129.
37. Mace ES, Buhariwalla KK, Crouch JH (2003) A high-throughput DNA extraction protocol for tropical molecular breeding programs. Plant Mol Biol Rep 21: 459-460.
38. Mann JA, Kimber CT, Miller FR (1983) The origin and early cultivation of sorghum in Africa. Texas Agricultural Experimental Station Bulletin, vol 1454. Texas A&M University, College Station.
39. Manzelli M, Pileri L, Lacerenza N, Benedettelli S, Vecchio V (2007) Genetic diversity assessment in Somalia sorghum (Sorghum bicolor (L.) Moench) accessions using microsatellite markers. Biodivers Conserv 16: 1715-1730.
40. McGuire S (2000) Farmers' management of sorghum diversity in Eastern Ethiopia. In: Almekinder CJM, de Boef W (eds) Encouraging diversity: the conservation and development of plant genetic resources. Intermediate Technology, London, pp 43-48.
41. McGuire S (2002) Farmers' view and management of sorghum diversity in Western Harerghe, Ethiopia: implications for collaboration with formal breeding. In: Cleveland DA, Soleri D (eds) Farmers, scientist and plant breeding. CAB International, pp 107.
42. Mekbib F (2008) Genetic erosion of sorghum (Sorghum bicolor (L.) Moench) in the centre of diversity, Ethiopia. Genet Resour Crop Evol 55: 351-364.
43. Menz MA, Klein RR, Unruh NC, Rooney WL, Klein PE, Mullet JE (2004) Genetic diversity of public inbreeds of sorghum determined by mapped AFLP and SSR markers. Crop Sci 44: 1236-1244.
44. Nei M, Tajima F, Tateno Y (1983) Accuracy of estimated phylogenetic trees from molecular data II. Gene frequency data. J Mol Evol 19: 153-170.
45. 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.
46. Pederson JF, Toy JJ, Johnson B (1998) Natural outcrossing of sorghum and sudangrass in the Central Great Plains. Crop Sci 38: 937-939.
47. Peel D, Ovenden JR, Peel SL (2004) NeEstimator: software for estimating effective population size, Version 1. 3. Queensland Government, Department of Primary Industries and Fisheries.
48. Petit RJ, El Mousadick A, Pons O (1998) Identifying populations for conservation on the basis of genetic markers. Conserv Biol 12: 844-855.
49. Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics 155: 945-959.
50. Prom LK, Erpelding J, Perumal R, Isakeit T, Cuevas HE (2012) Response of sorghum accessions from four African countries against Colletotrichum sublineolum, causal agent of sorghum anthracnose. Am J Plant Sci 3: 125-129.
51. Schuelke M (2000) An economic method for the fluorescent labeling of PCR fragments. Nat Biotechnol 18: 233-234.
52. Snowden JD (1936) The cultivated races of Sorghum. Adlard and Son, London.
53. Stemler ABL, Harlan JR, de Wet JMJ (1977) The sorghums of Ethiopia. Econ Bot 31: 446-460.
54. Taffesse AS, Dorosh P, Asrat S (2011) Crop production in Ethiopia: regional patterns and trends. Ethiopia strategy support program II (ESSP II): Working paper no. 0016.
55. Teshome A, Baum BR, Fahrig L, Torrance JK, Arnason TJ, Lambert JD (1997) Sorghum (Sorghum bicolor (L.) Moench) landraces variation and classification in north Shewa and south Welo, Ethiopia. Euphytica 97: 255-263.
56. 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.
57. Upadhyaya HD, Pundir RPS, Dwivedi SL, Godwa CLL, Gopal Reddy V, Singh S (2009) Developing mini core collection of sorghum (Sorghum bicolor (L.) Moench) for diversified utilization of germplasm. Crop Sci 49: 1769-1780.
58. Wang ML, Dean R, Erpelding JE, Pederson G (2006) Molecular genetic evaluation of sorghum germplasm differing in response to fungal diseases: rust (Puccinia purpurea) and anthracnose (Collectotrichum graminicola). Euphytica 148: 319-330.
59. 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.
60. Yao D, Myriam H, Mohammed T, Claude L, Xavier V (2004) In situ estimation of out crossing rate in sorghum landraces using micro-satellite markers. Euphytica 138: 205-212.
61. Zhu C, Gore M, Buckler ES, Yu J (2008) Status and prospect of association mapping in plants. Plant Genome 1: 5-20.