Browse > Article
http://dx.doi.org/10.7740/kjcs.2013.58.4.336

Analysis of the Genetic Diversity and Population Structure of Amaranth Accessions from South America Using 14 SSR Markers  

Oo, Win Htet (Department of Plant Resources, College of Industrial Sciences, Kongju National University)
Park, Yong-Jin (Center for Crop Genetic Resources and Breeding, Kongju National University)
Publication Information
KOREAN JOURNAL OF CROP SCIENCE / v.58, no.4, 2013 , pp. 336-346 More about this Journal
Abstract
Amaranth (Amaranthus sp. L.) is an important group of plants that includes grain, vegetable, and ornamental types. Centers of diversity for Amaranths are Central and South America, India, and South East Asia, with secondary centers of diversity in West and East Africa. The present study was performed to determine the genetic diversity and population structure of 75 amaranth accessions: 65 from South America and 10 from South Asia as controls using 14 SSR markers. Ninety-nine alleles were detected at an average of seven alleles per SSR locus. Model-based structure analysis revealed the presence of two subpopulations and 3 admixtures, which was consistent with clustering based on the genetic distance. The average major allele frequency and polymorphic information content (PIC) were 0.42 and 0.39, respectively. According to the model-based structure analysis based on genetic distance, 75 accessions (96%) were classified into two clusters, and only three accessions (4%) were admixtures. Cluster 1 had a higher allele number and PIC values than Cluster 2. Model-based structure analysis revealed the presence of two subpopulations and three admixtures in the 75 accessions. The results of this study provide effective information for future germplasm conservation and improvement programs in Amaranthus.
Keywords
Amaranth; genetic diversity; population structure; SSRs;
Citations & Related Records
연도 인용수 순위
  • Reference
1 Bao, J. S., H. Corke, and M. Sun. 2006. Analysis of genetic diversity and relationship in waxy rice (Oryza sativa L.) using AFLP and ISSR marker. Genetic Resources and Crop Evolution. 53 : 323-330.   DOI
2 Barbara, K. E., T. M. Haley, K. A. Willis, and G.M. Santangelo. 2007. The transcription factor Gcr1 stimulates cell growth by participating in nutrient-responsive gene expression on a global level. Molecular Genetics and Genomics. 277 : 171-188.   DOI
3 Bressani, R., J. M. Gonzales, J. Zuniga, M. Brauner, and L.G. Elias. 1987. Yield, selected chemical composition and nutritive value of 14 selections of amaranth grain representing four species. Journal of the Science of Food and Agriculture. 38 : 347-356.   DOI
4 Brien, O. G. K. and M. L. Price. 2008. Amaranth grain and vegetable types. www.echonet.org
5 Chan, K. F. and M. Sun. 1997. Genetic diversity and relationships detected by isozyme and RAPD analysis of crop and wild species of Amaranthus. Theor Appl Genet. 95 : 865-873   DOI
6 Costea, M., S. E. Weaver, and F. J. Tardif. 2004. The biology of Canadian weeds. 130. Amaranthus retroflexus L., A. powellii S. Watson and A. hybridus L. Can. J. Plant Sci. 84 : 631-668.   DOI   ScienceOn
7 Dodok, L., A. A. Modhir, V. Buchtova, G. Halasova, and I. Polacek. 1997. Importance and utilization of amaranth in food industry. Composition of amino acids and fatty acids. Nahrung. 41 : 108-110.   DOI   ScienceOn
8 Espitia Rangel, E. 1986. Caracterizacion y evaluacion preliminar de germoplasma de Amaranthus spp. Thesis (Ingeniero Agronomo) Universisdad Autonoma Agraria "Antonio Narro," Chapingo, Mexico. p. 105.
9 Evanno, G., S. Regnaut, and J. Goudet. 2005. Detecting the number of clusters of individuals using the software STRUCTURE a simulation study. Mol. Ecol.14 : 2611-2620.   DOI   ScienceOn
10 Falush, D., M. Stephens, and J. K. Pritchard. 2003. Inference of population structure using multilocus genotype data: linked loci and correlated allele frequencies. Genetics. 164 : 1567-1587.
11 Feltus, F. A., J. Wan, S. R. Schulze, J. C. Estill, N. Jiang, and A. H. Paterson. 2004. An SNP resource for rice genetics and breeding based on subspecies indica and japonica genome alignments. Genome Res. 14 : 1812-1819.   DOI   ScienceOn
12 Gamel, T. H., J. P. Linssen, A. S. Mesallam, A. A. Damir, and L. A. Shekib. 2006. Seed treatments affect functional and anti-nutritional properties of amaranth flours. J. Sci. Food. Agric. 86 : 1095-1102.   DOI   ScienceOn
13 Herrera T. G., Dp. Duque, I. P. Almeida, G. T, A. J. Pieters, C. P. Martinez, and J. M. Tohme. 2008. Assessment of genetic diversity in Venezuelan rice cultivars using simple sequence repeats markers. Electronic J. Biotechnol. 11.
14 Jarvis, D. I. and T. Hodgkin. 1998. Wild relatives and crop cultivars: conserving the connection. In: N. Zencirci, Z. Kaya, Y. Anikster, and W. T. Adams (eds). The Proceedings of an International Symposium on in Situ Conservation of Plant Genetic Diversity, Central Research Institute for Field Crops, Ankara, Turkey. p. 73-80.
15 Jarvis, D. I. and T. Hodgkin. 1999. Wild relatives and crop cultivars: detecting natural introgression and farmer selection of new genetic combinations in agroecosystems. Mol. Ecol. 8 : 159-173.   DOI   ScienceOn
16 Lewers K. S., S. M. N. Styan, S. C. Hokanson, and N. V. Bassil. 2005. Strawberry GenBank-derived and genomic simple sequence repeat (SSR) markers and their utility with strawberry, blackberry, and red and black raspberry. Journal of the American Society for Horticultural Science. 130 : 102-115.
17 Khaing, A. A., T. M. Kyaw, J. W. Chung, H. J. Baek, and Y. J. Park. 2013. Genetic diversity and population structure of the selected core set in Amaranthus using SSR markers. Plant Breeding. 132 : 165-173.   DOI   ScienceOn
18 Lanoue K. Z., P. G. Wolf, S. Browning, and E. E. Hood. 1996. Phylogenetic analysis of restriction site variation in wild and cultivated Amaranthus species (Amaranthaceae). Theor Appl Genet. 93 : 722-732.
19 Lee, J. R., G. Y. Hong, A. Dixit, J. W. Chung, K. H. Ma, J. H. Lee, H. K. Kang, Y. H. Cho, J. G. Gwag, and Y. J. Park. 2008. Characterization of microsatellite loci developed for Amaranthus hypochon-driacus and their cross-amplifi cations in wild species. Conserv. Genet. 9 : 243-246.   DOI   ScienceOn
20 Li, G., S. W. Kwon, and Y. J. Park. 2012. Updates and perspectives on the utilization of molecular makers of complex traits in rice. Genetics and Molecular Research 11 (4) : 4157-4168.   DOI   ScienceOn
21 Liu, K. and S. V. Muse. 2005. PowerMarker: an integrated analysis environment for genetic marker analysis. Bioinformatics. 21 : 2128 -2129.   DOI   ScienceOn
22 Liu, K. and S. V. Muse. 2005. PowerMarker: an integrated analysis environment for genetic marker analysis. Bioinformatics. 21 : 2128-2129.   DOI   ScienceOn
23 Moe, K. T., W. Zhao, H. S. Song, Y. H. Kim, J. W. Chung, Y. I. Cho, P. H. Park, H. S. Park, S. C. Chae, and Y. J. Park. 2010. Development of SSR markers to study diversity in the genus Cymbidium. Biochem. Syst. Ecol. 38 : 585-594.   DOI   ScienceOn
24 Oke, O. L. 1983. Amaranth. In: Handbook of tropical food. Chan Jr., P.I. Mariel (Eds.) Dekker, Inc. New York. pp : 55-56.
25 Mujica, A. and S. E. Jacobsen. 2003: The genetic resources of Andean grain amaranths (Amaranthus caudatus L., A. cruentus L. and A. hypo-chondriacus L.) in America. Plant Genet. Resour. Newsl. 133 : 41-44.
26 Nagaraju, J. and M. Kathirvel. 2002. Genetic analysis of traditional and evolved Basmati and non-Basmati rice varieties by using fluorescence-based ISSR-PCR and SSR markers. Proceedings of the National Academy of Sciences. 99(9) : 5836-5841.   DOI   ScienceOn
27 Nei, M. 1973. Analyses of gene diversity in subdivided populations. Proc. Natl. Acad. Sci., USA. 70 : 3321-3323.   DOI   ScienceOn
28 Ostrowski, M. F., A. David, S. Santoni, H. Mckhann, X. Reboud, V. L. Corre, C. Camilleri, D. Brunel, D. Bouchez, B. Faure, and T. Bataillon. 2006. Evidence for a large-scale population structure among accessions of Arabidopsis thaliana: possible causes and consequences for the distribution of linkage disequilibrium. Mo. Ecol. 15 : 1507-1517.   DOI   ScienceOn
29 Pritchard, J. K., M. Stephens, and P. Donnelly. 2000. Inference of population structure using multilocus genotype data. Genetics. 155 : 945-959.
30 Rousseau-Gueutin M. R., E. Lerceteau-Kohler, L. Barrot, D. J. Sargent, A. Monfort, D. Simpson, P. Arus, G. Guerin, and B. Denoyes-Rothan. 2008. Comparative genetic mapping between octoploid and diploid Fragaria species reveals a high level of colinearity between their genomes and the essentially disomic behavior of the cultivated octoploid strawberry. Genetics. 179 : 2045-2060.   DOI   ScienceOn
31 Sauer, J. D. 1950. The grain amaranths: a survey of their history and classification. Annals of the Missouri Botanical Garden. 37 : 561-619.   DOI   ScienceOn
32 Stallknecht, G. F. and J. R. Schulz-Schaeffer. 1993. Amaranth rediscovered. In: Janick J, Simon JE, editors. New crops. New York: Wiley. p. 211-218.
33 Sauer, J. D. 1967. The grain amaranths and their relatives: a revised taxonomic and geographic survey. Annals of MissouriBotanical Garden. 54 : 103-137.   DOI   ScienceOn
34 Schneider, S. and 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 Schuelke, M. 2000. An economic method for the fluorescent labeling of PCR products. Nat. Biotechnol. 18 : 233-234.   DOI   ScienceOn
36 Suh, H. S., Y. I. Sato, and H. Morishima. 1997. Genetic characterization of weedy rice (Oryza sativa L.) based on morpho-physiology, isozymes and RAPD markers. Theor. Appi. Genet. 94 : 316-321.   DOI   ScienceOn
37 Sun, M., H. Chen, and F. C. Leung. 1999. Low-cot sequences for fingerprinting analysis of germplasm diversity and relationships in Amaranthus. Theo Appl Genet. 99 : 464- 472.   DOI   ScienceOn
38 Tam, S. M., C. Mhiri, A. Vogelaar, M. Kerkveld, S. R. Pearce, and M. A. Grandbastien. 2005. Comparative analysis of genetic diversities within tomato and pepper collections detected by retrotransposon-based SSAP, AFLP and SSR. Theoretical and Applied Genetics. 110 : 819-831.   DOI   ScienceOn
39 Tamura, K., J. Dudley, M. Nei, and S. Kumar. 2007. MEGA4: molecular evolutionary genetics analysis (MEGA) software version 4.0. Mol. Biol. 24 : 1596 -1599.
40 Teutenico, R. A. and D. Knorr. 1985. Amaranth: Composition, properties, and applications of a rediscovered food crop. Food Technol. 39 : 49-60.
41 Zhao, W., J. W. Chung, K. H. Ma, T. S. Kim, S. M. Kim, D. I. Shin, C. H. Kim, H. M. Koo, and Y. J. Park. 2009. Analysis of genetic diversity and population structure of rice cultivars from Korea, China and Japan using SSR markers. Genes Genom. 31 : 283-292.   DOI   ScienceOn
42 Tucker, J. B. 1986. Amaranth: the once and future crop. Bio-Science. 36 : 9-13.
43 Xu, F. X. and M. Sun. 2001. Comparative analysis of phylogenetic relationships of grain amaranths and their wild relatives (Amaranthus; Amaranthaceae) using internal transcribed spacer, amplified fragment length polymorphism, and double-primer fluorescent intersimple sequence repeat markers. Molecular Phylogenetics and Evolution. 21(3) : 372-387.   DOI   ScienceOn