Development of a core set from a large rice collection using a modified heuristic algorithm to retain maximum diversity

Journal of Integrative Plant Biology

Volumn 51, Issue 12, 2009, Pages 1116-1125

  Chung, Hun Ki ^a   Kim, Kyu Won ^a   Chung, Jong Wook ^b   Lee, Jung Ro ^a   Lee, Sok Young ^a   Dixit, Anupam ^c   Kang, Hee Kyoung ^b   Zhao, Weiguo ^b,d   McNally, Kenneth L ^e   Hamilton, Ruraidh S ^e   Gwag, Jae Gyun ^a   Park, Yong Jin ^b  

^a National Academy of Agricultural Science   (South Korea)

^b Kongju National University   (South Korea)

^c SARDAR VALLABHBHAI PATEL UNIVERSITY OF AGRICULTURE AND TECHNOLOGY   (India)

^d JIANGSU UNIVERSITY OF SCIENCE AND TECHNOLOGY   (China)

^e INTERNATIONAL RICE RESEARCH INSTITUTE   (Philippines)

Author keywords

Core collection; Genetic diversity; Heuristic core collection; Oryza sativa; Sampling strategy

Indexed keywords

ALGORITHM; CLUSTER ANALYSIS; GENETIC ANALYSIS; GENOTYPE; HEURISTICS; RICE; SAMPLING;

ALGORITHM; ALLELE; ARTICLE; BIODIVERSITY; GENETICS; RICE;

ALGORITHMS; ALLELES; BIODIVERSITY; ORYZA SATIVA;

ORYZA SATIVA;

EID: 77249120576     PISSN: 16729072     EISSN: 17447909     Source Type: Journal    
DOI: 10.1111/j.1744-7909.2009.00882.x     Document Type: Article

References (35)

1. Abadie T, Magalhaes JR, Parentoni SN, Cordeiro C, de Andrade RV. (1999). The core collection of maize germplasm of Brazil. Plant Genet. Resour. News l 117, 55-56.
2. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. (1990). Basic local alignment search tool. J. Mol. Biol. 215, 403-410.
3. Balfourier F, Prosperi JM, Charmet G, Goulard M, Monestiez P. (1999). Using spatial patterns of diversity to develop core collections. In: Johnson RC, Hodgkin T, eds. Core Collections for Today and Tomorrow. International Plant Genetic Resources Institute, Rome. pp. 37-48.
4. Besemer J, Borodovsky M. (2005). GeneMark: web software for gene finding in prokaryotes, eurkaryotes and viruses. Nucleic Acids Res. 33(Web Server Issue), W451-W454.
5. Bretting PK, Widrlechner MP. (1995). Genetic markers and plant genetic resources management. Plant Breed. Rev. 13, 11-86.
6. Brown AHD. (1989a). Core collections: a practical approach to genetic resources management. Genome 31, 818-824.
7. Brown AHD. (1989b). The case for core collections. In: Brown AHD, Frankel OH, Marshal DR, Williams JT, eds. The Use of Plant Genetic Resources. Cambridge University Press, Cambridge. pp. 136-156.
8. Chandra S, Huaman Z, Hari Krishna S, Ortiz R. (2002). Optimal sampling strategy and core collection size of Andean tetraploid potato based on isozyme data-a simulation study. Theor. Appl. Genet. 104, 1325-1334.
9. Crossa J, Taba S, Eberhart SA, Bretting P, Vencovsky R. (1994). Practical considerations for maintaining germplasm in maize. Theor. Appl. Genet. 89, 89-95.
10. Diwan N, McIntosh MS, Bauchan GR. (1995). Methods of developing a core collection of annual Medicago species. Theor. Appl. Genet. 90, 755-761.
11. Franco J, Crossa J, Taba S, Shands H. (2003). A multivariate method for classifying cultivars and studying group x environment x trait interaction. Crop Sci. 43, 1249-1258.
12. Franco J, Crossa J, Warburton ML, Taba S. (2006). Sampling strategies for conserving maize diversity when forming core subsets using genetic markers. Crop Sci. 46, 854-864.
13. Frankel OH. (1984). Genetic perspectives of germplasm conservation. In: Arber W, Llimensee K, Peacock WJ, Starlinger P, eds. Genetic Manipulation: Impact on Man and Society. Cambridge University Press, Cambridge. pp. 161-170.
14. Gouesnard B, Bataillon TM, Decoux G, Rozale C, Schoen DJ, David JL. (2001). MSTRAT: an algorithm for building germplasm core collections by maximizing allelic or phenotypic richness. J. Hered. 92, 93-94.
15. Grenier C, Hamon P, Bramel-Cox PJ. (2001). Core collection of Sorghum: II. comparison of three random sampling strategies. Crop Sci. 41, 241-246.
16. Hu J, Zhu J, Xu XM. (2000). Methods of constructing core collections by stepwise clustering with three sampling strategies based on the genotypic values of crops. Theor. Appl. Genet. 101, 264-268.
17. Jansen J, van Hintum T. (2007). Genetic distance sampling: a novel sampling method for obtaining core collections using genetic distances with an application to cultivated lettuce. Theor. Appl. Genet. 114, 421-428.
18. Karg RL, Thompson GL. (1964) A heuristic approach to solving the traveling-salesman problem. Manage. Sci. 10, 225-248.
19. Kim KW, Chung HK, Cho GT, Ma KH, Chandrabalan D, Gwag JG et al. (2007). PowerCore: a program applying the advanced M strategy with a heuristic search for establishing core sets. Bioinformatics 23, 2155-2162.
20. Malosetti M, Abadie T. (2001). Sampling strategy to develop a core collection of Uruguayan maize landraces based on morphological traits. Genet. Resour. Crop. Evol. 48, 381-390.
21. McKhann HI, Camilleri C, Berard A, Bataillon T, David JL, Reboud X et al. (2004). Nested core collections maximizing genetic diversity in Arabidopsis thaliana. Plant J. 38, 193-202.
22. Nei M. (1978). Estimation of average heterozygosity and genetic distance from a small number of individuals. Genetics 89, 583-590.
23. Pearson K. (1895). Mathematical contributions to the theory of evolution, II: Skew variation in homogeneous material. Philos. Trans. Roy. Soc. London (A) 186, 343-414.
24. Peeters JP, Martinelli JA. (1989). Hierarchical cluster analyses as a tool to manage variation in germplasm collections. Theor. Appl. Genet. 78, 42-48.
25. Raymond TC. (1969). Heuristic algorithm for the traveling-salesman problem. IBM J. Res. Develop. 6, 400-407.
26. Schoen DJ, Brown AHD. (1993). Conservation of allelic richness in wild crop relatives is aided by assessment of genetic markers. Proc. Natl. Acad. Sci. USA 90, 10623-10627.
27. Shannon CE, Weaver W. (1949). The Mathematical Theory of Communication. University of Illinois Press, Urbana, IL.
28. Slater GS, Birney E. (2005). Automated generation of heuristics for biological sequence comparison. BMC Bioinformatics 6, 31.
29. Spagnoletti Zeuli PL, Qualset CO. (1993). Evaluation of five strategies for obtaining a core subset from a large genetic resource collection of durum wheat. Theor. Appl. Genet. 87, 295-304.
30. SPSS 13.0. (2004). Brief Guide. SPSS Inc., USA. pp. 1-255.
31. Sturges HA. (1926). The choice of a class-interval. J. Amer. Statist. Assoc. 21, 65-66.
32. Tai PYP, Miller JD. (2001). A core collection for Saccharum spontaneum L. from the world collection of sugarcane. Crop Sci. 41, 879-885.
33. van Hintum T, van Treuren R. (2002). Molecular markers: tools to improve genebank efficiency. Cell Mol. Biol. Lett. 7, 737-744.
34. Wang C, Lefkowitz EJ. (2005). Genomic multiple sequence alignments: refinement using a genetic algorithm. BMC Bioinformatics 6, 200.
35. Wang JC, Hu J, Liu NN, Xu HM, Zhang S. (2006). Investigation of combining plant genotypic values and molecular marker information for constructing core subsets. J. Integr. Plant Biol. 48, 1371-1378.