A core collection and mini core collection of Oryza sativa L. in China

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• 作者：Hongliang Zhang (1)
  Dongling Zhang (1)
  Meixing Wang (1)
  Junli Sun (1)
  Yongwen Qi (1)
  Jinjie Li (1)
  Xinghua Wei (2)
  Longzhi Han (3)
  Zongen Qiu (3)
  Shengxiang Tang (2)
  Zichao Li (1)
  
• 刊名：Theoretical and Applied Genetics
• 出版年：2011
• 出版时间：January 2011
• 年：2011
• 卷：122
• 期：1
• 页码：49-61
• 全文大小：753KB
• 参考文献：1. Allard RW (1992) Predictive methods for germplasm identification. In: Stalker HT, Murphy JP (eds) Plant breeding in the 1990’s. CAB International, Wallingford, pp 119-46
  2. Bataillon TM, David JL, Schoen DJ (1996) Neutral genetic markers and conservation genetics: simulated germplasm collections. Genetics 144:409-17
  3. Bisht IS, Mahajan RK, Lokknathan TR, Agrawal RC (1998) Diversity in Indian sesame collection and stratification of germplasm accessions in different diversity groups. Genet Resour Crop Evol 45:325-35 CrossRef
  4. Brown AHD (1978) Isozymes, plant population genetic structure and genetic conservation. Theor Appl Genet 52:145-57 CrossRef
  5. Brown AHD (1989a) The case for core collections. In: Brown AHD, Frankel OH, Marshall DR, Williams JT (eds) The use of plant genetic resources. Cambridge University Press, Cambridge, pp 136-56
  6. Brown AHD (1989b) Core collections: a practical approach to genetic resources management. Genome 31:818-24
  7. Charmet G, Balfourier F (1995) The use of geostatistics for sampling a core collection of perennial ryegrass populations. Genet Resour Crop Evol 42:303-09 CrossRef
  8. Crossa J, Hernandez M, Bretting P, Eberhart SA, Taba S (1993) Statistical genetic considerations for maintaining germplasm collections. Theor Appl Genet 86:637-78 CrossRef
  9. Ellis PR, Pink DAC, Phelps K, Jukes PL, Breeds SE, Pinnegar AE (1998) Evaluation of a core collection of / Brassica oleracea accessions for resistance to / Brevicoryne brassicae, the cabbage aphid. Euphytica 103:149-60 CrossRef
  10. Falush D, Stephens M, Pritchard JK (2003) Inference of population structure using multilocus genotype data: linked loci and correlated allele frequencies. Genetics 164:1567-587
  11. FAO (1997) Report on the State of the World’s Plant Genetic Resources for Food and Agriculture. Food and Agriculture Organization of the United Nations, Rome
  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 46:854-64 CrossRef
  13. Frankel OH, Brown AHD (1984) Plant genetic resources today: a critical appraisal. In: Holden JHW, Williams JT (eds) Crop genetic resources: conservation and evaluation. Allen and Unwin, London, pp 249-57
  14. Frankel OH, Brown AHD, Burdon JJ (1995) The conservation of plant biodiversity. Cambridge University Press, UK
  15. 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 92:93-4 CrossRef
  16. Holbrook CC, Timper P, Xue HQ (2000) Evaluation of the core collection approach for identifying resistance to / Meloidogyne arenaria in peanut. Crop Sci 40:1172-175 CrossRef
  17. Hyams D (2003) CurveExpert 1.3. A comprehensive curve fitting system for windows. http://curveexpert.webhop.net/
  18. Kashi Y, King DG (2006) Simple sequence repeats as advantageous mutators in evolution. Trends Genet 22:253-59 CrossRef
  19. Kim KW, Chung HK, Cho GT, Ma KH, Chandrabalan D, Gwag JG, Kim TS, Cho EG, Park YJ (2007) PowerCore: a program applying the advanced M strategy with a heuristic search for establishing core sets. Bioinformatics 23:2155-162 CrossRef
  20. Li ZC, Zhang HL, Zeng YW, Yang ZY, Shen SQ, Sun CQ, Wang XK (2002) Studies on sampling strategies for establishment of core collection of rice landrace in Yunnan, China. Genet Resour Crop Evol 49:67-4 CrossRef
  21. Li ZC, Zhang HL, Cao YS, Qiu ZE, Wei XH, Tang SX, Yu P, Wang XK (2003) Studies on the sampling strategy for primary core collection of Chinese indigence. Acta Agron Sin 29:20-4
  22. Liu K, Muse S (2004) PowerMarker: new genetic data analysis software, version 2.7. http://www.powermarker.net/
  23. Malvar RA, Butron A, Alvarez A, Ordas B, Soengas P, Revilla P, Ordas A (2004) Evaluation of the European Union maize landrace core collection for resistance to / Sesamia nonagrioides (Lepidoptera: Noctuidae) and / Ostrinia nubilalis (Lepidoptera: Crambidae). J Econ Entomol 97:628-34 CrossRef
  24. Morgan PH, Mercer LP, Flodin NW (1975) A general model for nutritional responses of higher organisms. Proc Natl Acad Sci USA 72:4327-331 CrossRef
  25. Noirot M, Hamon S, Anthony F (1996) The principal component scoring: a new method of constituting a core collection using quantitative data. Genet Resour Crop Evol 43:1- CrossRef
  26. Oka HI (1988) Origin of cultivated rice. Jnp. Sci. Soc. Press, Tokyo
  27. Panaud O, Chen XL, McCouch SR (1996) Development of microsatellite markers and characterization of simple sequence length polymorphism (SSLP) in rice ( / Oryza sativa L.). Mol Gen Genet 252:597-07
  28. Peeters JP, Martinelli JA (1989) Hierarchical cluster analysis as a tool to manage variation in germplasm collections. Theor Appl Genet 78:1142-148 CrossRef
  29. Qi YW (2007) Analysis of the genetic diversity of the rice cultivars ( / Oryza sativa L.) using SSR and HD1, HD3a gene. PhD Dissertation, China Agricultural University, Beijing
  30. Saghai-Maroof MA, Soliman KM, Jorgensen RA, Allard RW (1984) Ribosomal DNA spacer length polymorphism in barley: mendelian inheritance, chromosomal location and population dynamics. Proc Natl Acad Sci USA 81:8014-018 CrossRef
  31. 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 90:10623-0627 CrossRef
  32. Spagnoletti PLZ, Qualset CO (1993) Evaluation of five strategies for obtaining a core subset from a large genetic resource collection of durum wheat. Theor Appl Genet 87:295-04 CrossRef
  33. Tautz D, Renz M (1984) Simple sequences are ubiquitous repetitive components of eukaryotic genomes. Nucleic Acids Res 12:4127-138 CrossRef
  34. van Hintum ThJL, Brown AHD, Spillane C, Hodgkin T (2000) Core collections of plant genetic resources. IPGRI Technical Bulletin No. 3. International Plant Genetic Resources Institute, Rome, Italy
  35. Wang MX, Zhang HL, Zhang DL, Qi YW, Fan ZL, Li DY, Pan DJ, Cao YS, Qiu ZE, Yu P, Yang QW, Wang XK, Li ZC (2008) Genetic structure of / Oryza rufipogon Griff. in China. Heredity 101:527-35 CrossRef
  36. Yonezawa K, Nomura T, Morishima H (1995) Sampling strategies for use in stratified germplasm collections. In: Hodgkin T, Brown AHD, van Hintum ThJL, Morales EAV (eds) Core collections of plant genetic resources. IPGRI, Wiley, Baffins Lane, pp 35-4
  37. Zhang HL, Sun JL, Wang MX, Liao DQ, Zeng YW, Shen SQ, Yu P, Mu P, Wang XK, Li ZC (2007) Genetic structure and phylogeography of rice landraces in Yunnan, China revealed by SSR. Genome 51:72-3 CrossRef
  38. Zhang DL, Zhang HL, Wang MX, Sun JL, Qi YW, Wang FM, Wei XH, Han LZ, Wang XK, Li ZC (2009) Genetic structure and differentiation of / Oryza sativa L. in China revealed by microsatellites. Theor Appl Genet 119:1105-117 CrossRef
  
• 作者单位：Hongliang Zhang (1)
  Dongling Zhang (1)
  Meixing Wang (1)
  Junli Sun (1)
  Yongwen Qi (1)
  Jinjie Li (1)
  Xinghua Wei (2)
  Longzhi Han (3)
  Zongen Qiu (3)
  Shengxiang Tang (2)
  Zichao Li (1)
  
  1. Key Laboratory of Crop Genomics and Genetic Improvement of Ministry of Agriculture, Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
  2. China National Rice Research Institute, Hangzhou, 310006, Zhejiang, China
  3. Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
  
• ISSN：1432-2242

文摘

The extent of and accessibility to genetic variation in a large germplasm collection are of interest to biologists and breeders. Construction of core collections (CC) is a favored approach to efficient exploration and conservation of novel variation in genetic resources. Using 4,310 Chinese accessions of Oryza sativa L. and 36 SSR markers, we investigated the genetic variation in different sized sub-populations, the factors that affect CC size and different sampling strategies in establishing CC. Our results indicated that a mathematical model could reliably simulate the relationship between genetic variation and population size and thus predict the variation in large germplasm collections using randomly sampled populations of 700-,500 accessions. We recommend two principles in determining the CC size: (1) compromising between genetic variation and genetic redundancy and (2) retaining the main types of alleles. Based on the most effective scheme selected from 229 sampling schemes, we finally developed a hierarchical CC system, in which different population scales and genetic diversities allow a flexible use of genetic resources. The CC, comprising 1.7% (932) of the accessions in the basic collection, retained more than 85% of both the SSR and phenotypic variations. A mini core collection, comprising 0.3% (189) of the accessions in the basic collection, retained 70.65% of the SSR variation and 76.97% of the phenotypic variation, thus providing a rational framework for intensive surveys of natural variation in complex traits in rice genetic resources and hence utilization of variation in rice breeding.