Analysis of Genetic Diversity and Population Structure of Rice Cultivars from the Americas using SSR Markers

다국어 초록 (Multilingual Abstract)

The population structure of domesticated rice can be influenced by the natural history of
populations of predomesticated ancestors as well as by the breeding system and complexity of breeding
practices exercised by humans. This study was conducted to assess the genetic diversity and population
structure of 78 American rice accessions using 29 simple sequence repeat markers. A total of 281 alleles
were detected, and the number of alleles per marker locus ranged from 2 to 24, with an average of 9.7.
The genetic diversity and polymorphism information content values averaged 0.69 and 0.66, with ranges
of 0.32 to 0.94 and 0.30 to 0.94, respectively. The average heterozygosity was 0.70. Model-based structure
analysis revealed the presence of three subpopulations, which is basically consistent with clustering
based on genetic distance. The results could be used for future rice allele mining, association mapping
and cloning of gene(s), germplasm conservation, and effective breeding programs.

참고문헌 (Reference)

1 Davierwala, A.P, "Use of three different marker systems to estimate genetic diversity of Indian elite rice varieties" 108 (108): 269-284, 2000

2 Garland, S.H, "The use of microsatellite polymorphisms for the identification of Australian breeding lines of rice (Oryza sativa L.)" 108 (108): 53-63, 1999

3 Flint-Garcia, S.A, "Structure of linkage disequilibrium in plants" 54 (54): 357-374, 2003

4 Park, Y.J, "Simple sequence repeat polymorphisms (SSRPs) for evaluation of molecular diversity and germplasm classification of minor crops" 14 (14): 4546-4569, 2009

5 Liu, X.C, "SSR heterogenic patterns of parents for marking and predicting heterosis in rice breeding" 4 (4): 263-268, 1998

6 Culp,T.W, "Public breeding in the southeast" 493-519, 1998

7 Liu, K, "PowerMarker: an integrated analysis environment for genetic marker analysis" 21 (21): 2128-2129, 2005

8 Lu, H, "Population structure and breeding patterns of 145 U.S. rice cultivars based on SSR marker analysis" 45 (45): 66-76, 2005

9 Bao, J.S, "Microsatellites in starchsynthesizing genes in relation to starch physicochemical properties in waxy rice (Oryza sativa L.)" 105 : 898-905, 2002

10 Zhou, H.F, "Microsatellite analysis of genetic diversity and population genetic structure of a wild rice (Oryza rufipogon Griff.) in China" 107 (107): 332-339, 2003

11 Tamura, K, "MEGA4: Molecular evolutionary genetics analysis (MEGA) software version 4.0" 24 (24): 1596-1599, 2007

12 Kwon, S.J, "Isolation and characterization of 21 microsatellite loci in Lycium chinense and cross-amplification in Lycium barbarum" 10 (10): 1557-1560, 2009

13 Ma, K.H, "Isolation and characteristics of eight novel polymorphic microsatellite loci from the genome of garlic (Allium sativum L.)" 122 (122): 355-361, 2009

14 Falush, D, "Inference of population structure using multilocus genotype data: Linked loci and correlated allele frequencies" 164 (164): 1567-1587, 2003

15 Pritchard, J.K, "Inference of population structure using multilocus genotype data" 155 (155): 945-959, 2000

16 Ostrowski, M.F, "Evidence for a large-scale population structure among accessions of Arabidopsis thaliana: possible causes and consequences for the distribution of linkage disequilibrium" 15 (15): 1507-1517, 2006

17 Park, Y.J, "Evaluation of genetic diversity and relationships within an on-farm collection of Perilla frutescens Britt. using microsatellite markers" 55 (55): 523-535, 2008

18 Chen, X, "Development of a microsatellite framework map providing genome-wide coverage in rice (Oryza sativa L.)" 95 (95): 553-567, 1997

19 Lee, G.A, "Development of SNP-based CAPS and dCAPS markers in eight different genes involved in starch biosynthesis in rice" 24 (24): 93-101, 2009

20 Evanno, G, "Detecting the number of clusters of individuals using the software structure: a simulation study" 14 (14): 2611-2620, 2005

21 Dilday, R.H, "Contribution of ancestral lines in the development of new cultivars of rice" 30 (30): 905-911, 1990

22 Temnykh, S, "Computational and experimental analysis of microsatellites in rice (Oryza sativa L.): frequency, length variation, transposon associations, and genetic marker potential" 11 (11): 1441-1452, 2001

23 Olufowote, J.O, "Comparative evaluation of within-cultivar variation of rice (Oryza sativa L.) using microsatellite and RFLP markers" 40 (40): 370-378, 1997

24 Lee, J.R, "Characterization of microsatellite loci developed for Amaranthus hypochondriacus and their cross-amplifications in wild species" 9 (9): 243-246, 2008

25 Zhao, X, "Characterization and genetic mapping of a short, highly repeated, interspersed DNA sequence from rice (Oryza sativa L.)" 231 (231): 353-359, 1992

26 Zhao, W.G, "Association analysis of the amino acid contents in rice" 51 (51): 1126-1137, 2009

27 Herrera, T.G, "Assessment of genetic diversity in Venezuelan rice cultivars using simple sequence repeats markers" 11 (11): 1-14, 2008

28 Weiguo Zhao, "Analysis of Genetic Diversity and Population Structure of Rice Cultivars from Korea, China and Japan using SSR Markers" 한국유전학회 31 (31): 283-292, 2009

29 Schuelke,M, "An economic method for the fluorescent labeling of PCR fragments" 18 (18): 233-234, 2000

30 Nei, M, "Accuracy of estimated phylogenetic trees from molecular data" 19 (19): 153-170, 1983

31 Yu, J.W, "A study on relative abundance, composition and length variation of microsatellites in eighteen underutilized crop species" 56 (56): 237-246, 2009