Characterization of indica–japonica subspecies-specific InDel loci in wild relatives of rice (Oryza sativa L. subsp. indica Kato and subsp. japonica Kato)
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Insertion/deletion (InDel) polymorphisms are generally irreversible and, thus, are useful for evaluating the genetic relationships within the genus Oryza. Moreover, subspecies-specific (SS) InDel markers linked to conserved genomic regions specific to the indica and japonica subspecies of Oryza sativa can provide insight into the genetic relationships between cultivated and wild rice. The evolutionary relationship among Oryza species in respect to their indica and japonica alleles was investigated using 67 selected indica–japonica InDel SS-STS primers across 290 accessions, including 61 Asian cultivated rice (O. sativa) cultivars, 27 African cultivated rice (O. glaberrima) accessions, and 202 accessions of wild Orzya species. The average SS allele frequency of the various Oryza species, from AA-genome to BB ~ EE, and FF ~ HHKK showed an increased proportion of non-O. sativa and null alleles in the more distantly related wild species. Most of the wild species, except the more distant EE, GG, HHJJ, and HHKK genome accessions, consisted of relatively more indica than japonica alleles of SS markers. To validate the SS-STS study, PCR products of nine markers were sequenced across 24–33 accessions. Sequencing results revealed that Oryza species share indica or japonica-like conserved InDel regions even across the different genomes. The presence of some japonica alleles beyond the AA genome at some SS InDel loci also suggests that japonica-specific alleles occurred early in the history of the Oryza genus. The O. sativa sub-species specific markers thus provide further insight into the evolutionary pathway in the genus Oryza and the process of differentiation between indica and japonica.
Keywordsindica–japonica Insertion-deletion markers Oryza Subspecies-specific markers Wild rice
This work was supported by a grant from the Next-Generation BioGreen 21 Program (Plant Molecular Breeding Center, No. PJ01102401), Rural Development Administration, Republic of Korea and support from the Global Rice Science Partnership (GRiSP) to the International Rice Research Institute. The authors thank Christine Jade Dilla-Ermita, Joie Ramos and Eleazar Manalaysay for providing technical support.
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Conflict of interest
The authors declare that they have no conflict of interest.
Human and animal rights
This research does not involve human participants or animals.
- Brar DS, Khush GS (2002) Transferring genes from wild species into rice. In: Kang MS (ed) Quantitative genetics, genomics, and plant breeding. CAB International, Wallingford, pp 197–217Google Scholar
- Chin JH, Kim HH, Jiang WZ, Chu SH, Woo MO, Han LZ, Brar DS, Koh HJ (2007) Identification of subspecies-specific STS markers and their association with segregation distortion in rice (Oryza sativa L.). J Crop Sci Biotech 10:175–184Google Scholar
- Huang X, Kurata N, Wei X, Wang ZX, Wang A, Zhao Q, Zhao Y, Liu K, Lu H, Li W, Guo Y, Zhou C, Fan D, Weng Q, Zhu C, Huang T, Lei Zhang, Wang Y, Feng L, Furuumi H, Kubo T, Miyabayash T, Yuan X, Xu Q, Dong G, Zhan Q, Li C, Fujiyama A, Toyoda A, Lu T, Feng Q, Qian Q, Li J, Han B (2012) A map of rice genome variation reveals the origin of cultivated rice. Nature 490:497–501CrossRefPubMedGoogle Scholar
- Kim BS, Jiang W, Koh HJ (2009) Genetic diversity of rice collections using subspecies-specific STS markers. Korean J Breed Sci 41:101–105Google Scholar
- Lu F, Ammiraju JSS, Sanyalc A, Zhanga S, Song R, Chena J, Lia G, Suia Y, Song X, Chenga Z, de Oliveira AC, Bennetzen JL, Jackson SA, Wing RA, Chena M (2009) Comparative sequence analysis of MONOCULM1-orthologous regions in 14 Oryza genomes. Proc Natl Acad Sci USA 106:2071–2076CrossRefPubMedPubMedCentralGoogle Scholar
- McCouch SR, Sweeney M, Li J, Jiang H, Thomson M, Septiningsih E, Edwards J, Moncada P, Xiao J, Garris A, Tai T, Martinez C, Tohme J, Sugiono M, McClung A, Yuan LP, Ahn SN (2007) Through the genetic bottleneck: O. rufipogon as a source of trait-enhancing alleles for O. sativa. Euphytica 154:317–339CrossRefGoogle Scholar
- Pal S, Jain S, Jain RK (2001) DNA isolation from milled rice samples for PCR based molecular marker analysis. Rice Genet News 18:94Google Scholar
- Thomson MJ, Zhao K, Wright M, McNally KL, Rey J, Tung CW, Reynolds A, Scheffler B, Eizenga G, McClung A, Kim H, Ismail AM, de Ocampo M, Mojica C, Reveche MY, Dilla-Ermita CJ, Mauleon R, Leung H, Bustamante C, McCouch SR (2012) High-throughput single nucleotide polymorphism genotyping for breeding applications in rice using the BeadXpress platform. Mol Breed 29:875–886Google Scholar
- Zhao K, Wright M, Kimball J, Eizenga G, McClung A, Kovach M, Tyagi W, Ali ML, Tung CW, Reynolds A, Bustamante CD, McCouch SR (2010) Genomic diversity and introgression in O. sativa reveal the impact of domestication and breeding on the rice genome. PLoS ONE 5:e10780CrossRefPubMedPubMedCentralGoogle Scholar