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Application of indica–japonica single-nucleotide polymorphism markers for diversity analysis of Oryza AA genome species

Published online by Cambridge University Press:  16 July 2014

Yoo-Jin Lee
Affiliation:
International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
Michael J. Thomson
Affiliation:
International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
Joong Hyoun Chin*
Affiliation:
International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
*
* Corresponding author. E-mail: j.chin@irri.org

Abstract

High-throughput genotyping using single-nucleotide polymorphisms (SNP) is one tool that can be used to study the genetic relationships between wild rice relatives and cultivated rice. In this study, a set of 96 indica–japonica SNP markers, which can differentiate indica and japonica subspecies of rice, were used to characterize 227 Oryza accessions including 93 AA genome accessions from seven wild Oryza species. A total of 72 markers of the 96 markers were selected for the phylogenetic study and allele polymorphism survey. A subset of SNP markers were present only in Oryza sativa and evolutionarily close species, Oryza nivara and Oryza rufipogon. These markers can be used for distinguishing cultivated rice from the other species and vice versa. Eight clusters were generated through phylogenetic analysis, and Oryza meridionalis and Oryza longistaminata appeared to be the most distantly related species to cultivated rice. In this study, Oryza barthii and Oryza glaberrima accessions were found to exhibit high genetic similarity. Across the wild species, more indica-type alleles were detected for most accessions. In this study, a set of markers selected to be informative across O. sativa accessions were used, but it will be interesting to compare the results of this study with SNP data obtained through next-generation sequencing in the future.

Type
Research Article
Copyright
Copyright © NIAB 2014 

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References

Garris, AJ, Tai, TH, Coburn, J, Kresovich, S and McCouch, S (2005) Genetic structure and diversity in Oryza sativa L. Genetics 169: 16311638.Google Scholar
Jacquemin, J, Bhatia, D, Singh, K and Wing, RA (2013) The International Oryza Map Alignment Project: development of genus-wide comparative genomics platform to help solve the 9 billion-people question. Current Opinion in Plant Biology 16: 147158.CrossRefGoogle ScholarPubMed
Liu, K and Muse, SV (2005) PowerMarker: an integrated analysis environment for genetic marker analysis. Bioinformatics 21: 21282129.CrossRefGoogle ScholarPubMed
McCouch, SR, Zhao, K, Wright, M, Tung, C-W, Ebana, K, Thomson, MJ, Reynold, A, Wang, D, DeClerck, G, Ali, ML, McClung, A, Eizenga, G and Bustamante, C (2010) Development of genome-wide SNP assays for rice. Breeding Science 60: 524535.Google Scholar
McNally, KL, Childs, KL, Bohnert, R, Davidson, RM, Zhao, K, Ulat, VJ, Zeller, G, Clark, RM, Hoen, DR, Bureau, TE, Stokowski, R, Ballinger, DG, Frazer, KA, Cox, DR, Padhukasahasram, B, Bustamante, CD, Weigel, D, Mackill, D, Bruskiewich, RM, Rätsch, G, Buell, CR and Leung, H (2009) Genomewide SNP variation reveals relationships among landraces and modern varieties of rice. Proceedings of the National Academy of Sciences of the USA 106: 1227312278.Google Scholar
Nei, M (1973) Analysis of gene diversity in subdivided populations. Proceedings of the National Academy of Sciences of the USA 70: 33213323.CrossRefGoogle ScholarPubMed
Tamura, K, Dudley, J, Nei, M and Kumar, S (2007) MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Molecular Biology and Evolution 24: 15961599.CrossRefGoogle ScholarPubMed
Thomson, MJ, Zhao, K, Wright, M, McNally, KL, Rey, J, Tung, C-W, Reynolds, A, Scheffler, B, Eizenga, G, McClung, A, Kim, H, Ismail, AM, de Ocampo, M, Mojica, C, Reveche, MY, Dilla, CJ, Mauleon, R, Leung, H, Bustamante, C and McCouch, SR (2012) High-throughput single nucleotide polymorphism genotyping for breeding applications in rice using the BeadXpress platform. Molecular Breeding 29: 875886.Google Scholar
Tung, C-W, Zhao, K, Wright, MH, Ali, ML, Jung, J, Kimball, J, Tyagi, W, Thomson, MJ, McNally, K, Leung, H, Kim, H, Ahm, S-N, Reynold, A, Scheffler, B, Eizenga, G, McClung, A, Bustamante, C and McCouch, SR (2010) Development of research platform for dissecting phenotype–genotype association in rice (Oryza spp.). Rice 3: 205217.CrossRefGoogle Scholar
Zhao, K, Wright, M, Kimball, J, Eizenga, G, McClung, A, Kovach, M, Tyagi, W, Ali, ML, Tung, C-W, Reynolds, A, Bustamante, CD and McCouch, SR (2010) Genomic diversity and introgression in O. sativa reveal the impact of domestication and breeding on the rice genome. PLoS One 5: e10780.CrossRefGoogle Scholar
Zhao, K, Tung, C-W, Eizenga, GC, Wright, M, Ali, ML, Price, AH, Norton, GJ, Islam, MR, Reynolds, A, Mezey, J, McClung, A, Bustamante, CD and McCouch, SR (2011) Genome-side association reveals a rich genetic architecture of complex traits in Oryza sativa . Nature Communications 13: 467.CrossRefGoogle Scholar
Zhu, Q and Ge, S (2005) Phylogenetic relationships among A-genome species of the genus Oryza revealed by intron sequences of four nuclear genes. New Phytologist 167: 249265.CrossRefGoogle ScholarPubMed
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