Genotypic and phenotypic characterization of genetic differentiation and diversity in the USDA rice mini-core collection

Genetica

Volumn 138, Issue 11, 2010, Pages 1221-1230

  Li, Xiaobai ^a,c,d   Yan, Wengui ^d   Agrama, Hesham ^c   Hu, Biaolin ^e   Jia, Limeng ^b,c,d   Jia, Melissa ^d   Jackson, Aaron ^d   Moldenhauer, Karen ^c   McClung, Anna ^d   Wu, Dianxing ^b  

^a ZHEJIANG UNIVERSITY   (China)

^b ZHEJIANG UNIVERSITY   (China)

^c UNIVERSITY OF ARKANSAS   (United States)

^d AGRICULTURAL RESEARCH SERVICE   (United States)

^e Jiangxi Academy of Agricultural Sciences   (China)

Author keywords

Differentiation; Diversity; Genotype; Mini core collection; Phenotype; Rice

Indexed keywords

ALLELE; ARTICLE; BREEDING; CLUSTER ANALYSIS; GENETIC DRIFT; GENETIC MARKER; GENETIC POLYMORPHISM; GENETIC VARIABILITY; GENETICS; GENOTYPE; GOVERNMENT; PHENOTYPE; PHYLOGENY; RICE; UNITED STATES;

ALLELES; BREEDING; CLUSTER ANALYSIS; GENETIC DRIFT; GENETIC MARKERS; GENETIC VARIATION; GENOTYPE; ORYZA SATIVA; PHENOTYPE; PHYLOGENY; POLYMORPHISM, GENETIC; UNITED STATES; UNITED STATES DEPARTMENT OF AGRICULTURE;

JAPONICA; ORYZA; ZIZANIA;

EID: 78650513629     PISSN: 00166707     EISSN: None     Source Type: Journal    
DOI: 10.1007/s10709-010-9521-5     Document Type: Article

References (53)

1. Abadie T, Cordeiro CMT, Fonseca JR, Alves RBN, Burle ML, Brondani C, Rangel PHN, Castro EM, Silva HT, Freire MS, Zimmermann FJP, Magalhaes JRSO (2005) Constructing a rice core collection for Brazil. Pesquisa Agropecu Bras 40: 129-136.
2. Agrama HA, Eizenga GC (2008) Molecular diversity and genome-wide linkage disequilibrium patterns in a worldwide collection of Oryza sativa and its wild relatives. Euphytica 160: 339-355.
3. Agrama HA, Yan WG (2009) Genetic diversity and relatedness of rice cultivars resistant to straighthead disorder. Plant Breed. doi: 10. 1111/j. 1439-0523. 2009. 01688. x.
4. Agrama HA, Yan WG, Lee F, Fjellstrom R, Chen MH, Jia M, McClung A (2009) Genetic assessment of a mini-core subset developed from the USDA rice Genebank. Crop Sci 49: 1336-1346.
5. Borba TCO, Brondani RPV, Rangel PHN, Brondani C (2005) Evaluation of the number and information content of fluorescent-labeled SSR for rice germplasm characterization. Crop Breed Appl Biotechnol 2: 157-165.
6. Borba TCO, Brondani RPV, Rangel PHN, Brondani C (2009) Microsatellite marker-mediated analysis of the EMBRAPA rice core collection genetic diversity. Genetica 137: 293-304.
7. Brondani C, Borba TCO, Rangel PHN, Brondani RPV (2006) Determination of traditional varieties of Brazilian rice using microsatellite markers. Genet Mol Biol 29: 676-684.
8. Brown AHD (1989) Core collections: a practical approach to genetic resources management. Genome 31: 818-824.
9. Cheng CY, Motohashi R, Tsuchimoto S, Fukuta Y, Ohstubo H, Ohtsubo E (2003) Polyphyletic origin of cultivated rice: based on the interspersion pattern of SINEs. Mol Biol Evol 20: 67-75.
10. 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.
11. Chu Y, Ramos L, Holbrook CC, Ozias-Akins P (2007) Frequency of a loss-of-function mutation in oleoyl-PC desaturase (ahFAD2A) in the mini-core of the US peanut germplasm collection. Crop Sci 47: 2372-2378.
12. Elias M, Penet L, Vindry P, McKey D, Panaud O, Robert T (2001a) Unmanaged sexual reporoduction and the dynamics of genetic diversity of a vegetatively propagated crop plant, cassava (Manihot esculenta Crantz), in a traditional farming system. Mol Eco 10: 1895-1907.
13. Elias M, McKey D, Panaud O, Anstett MC, Robert T (2001b) Traditional management of cassava morphological and genetic diversity by the Makushi Amerindians (Guyana, South America): perspectives for on-farm conservation of crop genetic resources. Euphytica 120: 143-157.
14. Evanno G, Regnaut S, Goudet J (2005) Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Mol Ecol 14: 2611-2620.
15. Garris AJ, Tai TH, Coburn J, Kresovich S, McCouch SR (2005) Genetic structure and diversity in Oryza sativa L. Genetics 169: 1631-1638.
16. Gaudeul M, Taberlet P, Till-Bottraud I (2000) Genetic diversity in an endangered alpine plant, Eryngium alpinum L. (Apiaceae), inferred from amplified fragment length polymorphism markers. Molecular Ecol 9: 1625-1637.
17. Gizaw S, van Arendonk JAM, Komen H, Windig JJ, Hanotte O (2007) Population structure, genetic variation and morphological diversity in indigenous sheep of Ethiopia. Anim Genet 38: 621-628.
18. Glaszmann JC (1987) Isozymes and classification of Asian rice varieties. Theor Appl Genet 74: 21-30.
19. Hamilton RS, Raymond R (2005) Toward a global strategy for the conservation of rice genetic resources. In: Toriyama K, Heong KL, Hardy B (eds) Rice is life: scientific perspectives for the 21st century. Proceedings of the world rice research conference held in Tsukuba, Japan, CD-ROM, pp 47-49.
20. Holbrook CC, Dong W (2005) Development and evaluation of a mini core collection for the US peanut germplasm collection. Crop Sci 45: 1540-1544.
21. Hossain M (2007) Rice facts: a balancing act. Rice Today 6: 37.
22. Jain S, Jain RK, McCouch SR (2004) Genetic analysis of Indian aromatic and quality rice (Oryza sativa L.) germplasm using panels of fluorescently-labeled microsatellite markers. Theor Appl Genet 109: 965-977.
23. Kouame CN, Quesenberry KH (1993) Cluster analysis of a world collection of red clover germplasm. Genet Res Crop Evo 40: 39-47.
24. Lewis PO, Zaykin D (2001) Genetic data analysis: computer program for the analysis of allelic data version 1. 0. http://lewis. eeb. uconn. edu/lewishome/software. html. Cited 21 Nov 2001.
25. Liang F, Deng Q, Wang Y, Xiong Y, Jin D, Li J, Wang B (2004) Molecular marker-assisted selection for yield-enhancing genes in the progeny of "9311 × O. rufipogon" using SSR. Euphytica 139: 159-165.
26. Liu K, Muse SV (2005) Powermarker: an integrated analysis environment for genetic marker analysis. Bioinformatics 21: 2128-2129.
27. Mackill DJ (1995) Plant genetic resources: classifying japonica rice cultivars with RAPD markers. Crop Sci 35: 889-894.
28. Mantel N (1967) The detection of disease clustering and a generalized regression approach. Cancer Res 27: 209-220.
29. Merilaè J, Crnokrak P (2001) Comparison of genetic differentiation at marker loci and quantitative traits. J Evol Biol 14: 892-903.
30. Nei M, Takezaki N (1983) Estimation of genetic distances and phylogenetic trees from DNA anlysis. Proc. 5th World Cong. Genet Appl Livstock Prod 21: 405-412.
31. Pande S, Kishore GK, Upadhyaya HD, Rao JN (2006) Identification of sources of multiple disease resistance in mini-core collection of chickpea. Plant Dis 90: 1214-1218.
32. Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics 155: 945-959.
33. Rohlf F (2000) NTSYS-PC numerical taxonomy and multivariate analysis system ver 2. 11L. Applied Biostatistics, NY.
34. Schneider S, Excoffier L (1999) Estimation of demographic parameters from the distribution of pairwise differences when the mutation rates vary among sites: application to human mitochondrial DNA. Genetics 152: 1079-1089.
35. Sharma R, Rao VP, Upadhyaya HD, Reddy VG, Thakur RP (2010) Resistance to grain mold and downy mildew in a mini-core collection of sorghum germplasm. Plant Dis 94: 439-444.
36. Sweeney MT, Thomson MJ, Pfeil BE, McCouch S (2006) Caught red-handed: Rc encodes a basic helix-loop-helix protein conditioning red pericarp in rice. Plant Cell 18: 283-294.
37. Tamura K, Dudley J, Nei M, Kumar S (2007) MEGA4: molecular evolutionary genetics analysis (MEGA) software version 4. 0. Mol Biol Evol 24: 1596-1599.
38. Tanksley S, McCouch SR (1997) Seed banks and molecular maps: unlocking genetic potential from the wild. Science 277: 1063-1066.
39. Thomson MJ, Septiningsih EM, Suwardjo F, Santoso TJ, Silitonga TS, McCouch SR (2007) Genetic diversity analysis of traditional and improved Indonesian rice (Oryza sativa L.) germplasm using microsatellite markers. Theor Appl Genet 114: 559-568.
40. Thomson MJ, Polato NR, Prasetiyono J, Trijatmiko KR, Silitonga TS, McCouch SR (2009) Genetic diversity of isolated populations of Indonesian landraces of rice (Oryza sativa L.) collected in east Kalimantan on the island of Borneo. Rice 2: 80-92.
41. Upadhyaya HD (2005) Variability for drought resistance related traits in the mini core collection of peanut. Crop Sci 45: 1432-1440.
42. Upadhyaya HD, Oritz R (2001) A mini-core collection for capturing diversity and promoting utilization of chickpea genetic resources in crop improvement. Theor Appl Genet 102: 1292-1298.
43. Upadhyaya HD, Reddy LJ, Gowda CLL, Reddy KN, Singh S (2006) Development of a mini core for enhanced and diversified utilization of pigeonpea germplasm resources. Crop Sci 46: 2127-2132.
44. Upadhyaya HD, Pundir RPS, Dwivedi SL, Gowda CLL, Reddy VG, Singh S (2009) Developing a mini core collection of sorghum for diversified utilization of germplasm. Crop Sci 49: 1769-1780.
45. Weir BS (1996) Genetic data analysis II: methods for discrete population genetic data. Sinauer assoc., Inc. Sunderland, MA.
46. Xin Z, Velten JP, Oliver MJ, Burke JJ (2003) Highthroughput DNA extraction method suitable for PCR. Biotechniques 34: 820-826.
47. Xu YB, Beachell H, McCouch SR (2004) A marker-based approach to broadening the genetic base of rice in the USA. Crop Sci 44: 1947-1959.
48. Yan W, Rutger JN, Bockelman HE, Tai TH. (2005a) Agronomic evaluation and seed stock establishment of the USDA rice core collection. In: RJ Norman et al. (ed.) BR wells rice research studies 2004. University of Arkansas, Agri Exp Sta Res Ser 529: 63-68.
49. Yan W, Rutger JN, Bockelman HE, Tai TH. (2005b). Evaluation of kernel characteristics of the USDA rice core collection. In: RJ Norman et al. (ed.) BR wells rice research studies 2004. University of Arkansas, Agri Exp Sta, Res Ser 529: 69-74.
50. Yan WG, Rutger JN, Bryant RJ, Bockelman HE, Fjellstrom RG, Chen MH, Tai TH, McClung AM (2007) Development and evaluation of a core subset of the USDA rice (Oryza sativa L.) germplasm collection. Crop Sci 47: 869-878.
51. Yan WG, Li Y, Agrama HA, Luo D, Gao F, Lu X, Ren G (2009) Association mapping of stigma and spikelet characteristics. Mol Breeding 24: 277-292.
52. Zeng Y, Shen S, Li Z, Yang Z, Wang X, Zhang H, Wen G (2003) Ecogeographic and genetic diversity based on morphological characters on indigenous rice (Oryza sativa L.) in Yunnan, China. Genet Res Crop Evo 50: 567-577.
53. Zhu C, Yu J (2009) Nonmetric multidimensional scaling corrects for population structure in whole genome association studies. Genetics 182: 875-888.