Introgression of the Chromosomal Region with the Pi-cd Locus from Oryza Meridionalis into O. Sativa L. During Rice Domestication

Overview

Journal Theor Appl Genet

Publisher Springer

Specialty Genetics

Date 2019 Mar 27

PMID 30911779

Citations 5

Authors

Kenji Fujino

Yuji Hirayama

Mari Obara

Tomohito Ikegaya

Affiliations

Soon will be listed here.

Abstract

The genotype of the Pi-cd locus found in blast-resistant rice variety Kitakurin, which is a cultivated rice from Japan belonging to Oryza sativa japonica, is identical to that of its wild relative O. meridionalis. Crop domestication from wild relatives to cultivated species has encompassed significant phenotypic changes. However, little is known about the genetic changes involved in domestication. Here, we surveyed the origin of the Pi-cd locus across Oryza species with AA genomes by comparison with the genome sequences of Hoshinoyume (HS), which does not carry the Pi-cd blast resistance gene, and Kitakurin (KK), which carries the Pi-cd blast resistance gene. We found that variety-specific transposons were enriched at the Pi-cd locus. The genotype of the Pi-cd locus characterized by transposons in HS and KK was specific to each Oryza species with the AA genome. The Kitaake (KT) genotype at the Pi-cd locus found in KK was identical only to that of O. meridionalis and distributed only in subgroups of japonica in the World Rice Collection and tropical japonica in the Japanese Rice Collection, whereas it was not present in O. rufipogon accessions. The distinct distributions of genotypes of the Pi-cd locus clearly demonstrated that the Pi-cd locus was introgressed from O. meridionalis into O. sativa, specific to tropical japonica.

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References

Rozen S, Skaletsky H . Primer3 on the WWW for general users and for biologist programmers. Methods Mol Biol. 1999; 132:365-86. DOI: 10.1385/1-59259-192-2:365. View

Vaughan D, Morishima H, Kadowaki K . Diversity in the Oryza genus. Curr Opin Plant Biol. 2003; 6(2):139-46. DOI: 10.1016/s1369-5266(03)00009-8. View

Fujino K, Sekiguchi H, Sato T, Kiuchi H, Nonoue Y, Takeuchi Y . Mapping of quantitative trait loci controlling low-temperature germinability in rice (Oryza sativa L.). Theor Appl Genet. 2003; 108(5):794-9. DOI: 10.1007/s00122-003-1509-4. View

Garris A, Tai T, Coburn J, Kresovich S, McCouch S . Genetic structure and diversity in Oryza sativa L. Genetics. 2005; 169(3):1631-8. PMC: 1449546. DOI: 10.1534/genetics.104.035642. View

Fujino K, Sekiguchi H, Kiguchi T . Identification of an active transposon in intact rice plants. Mol Genet Genomics. 2005; 273(2):150-7. DOI: 10.1007/s00438-005-1131-z. View

Wang G, He Y, Xu C, Zhang Q . Identification and confirmation of three neutral alleles conferring wide compatibility in inter-subspecific hybrids of rice (Oryza sativa L.) using near-isogenic lines. Theor Appl Genet. 2005; 111(4):702-10. DOI: 10.1007/s00122-005-2055-z. View

Wing R, Ammiraju J, Luo M, Kim H, Yu Y, Kudrna D . The oryza map alignment project: the golden path to unlocking the genetic potential of wild rice species. Plant Mol Biol. 2005; 59(1):53-62. DOI: 10.1007/s11103-004-6237-x. View

Londo J, Chiang Y, Hung K, Chiang T, Schaal B . Phylogeography of Asian wild rice, Oryza rufipogon, reveals multiple independent domestications of cultivated rice, Oryza sativa. Proc Natl Acad Sci U S A. 2006; 103(25):9578-83. PMC: 1480449. DOI: 10.1073/pnas.0603152103. View

Doebley J, Gaut B, Smith B . The molecular genetics of crop domestication. Cell. 2006; 127(7):1309-21. DOI: 10.1016/j.cell.2006.12.006. View

10.

Ross-Ibarra J, Morrell P, Gaut B . Plant domestication, a unique opportunity to identify the genetic basis of adaptation. Proc Natl Acad Sci U S A. 2007; 104 Suppl 1:8641-8. PMC: 1876441. DOI: 10.1073/pnas.0700643104. View

11.

Kovach M, McCouch S . Leveraging natural diversity: back through the bottleneck. Curr Opin Plant Biol. 2008; 11(2):193-200. DOI: 10.1016/j.pbi.2007.12.006. View

12.

Konishi S, Ebana K, Izawa T . Inference of the japonica rice domestication process from the distribution of six functional nucleotide polymorphisms of domestication-related genes in various landraces and modern cultivars. Plant Cell Physiol. 2008; 49(9):1283-93. DOI: 10.1093/pcp/pcn118. View

13.

Ammiraju J, Lu F, Sanyal A, Yu Y, Song X, Jiang N . Dynamic evolution of oryza genomes is revealed by comparative genomic analysis of a genus-wide vertical data set. Plant Cell. 2008; 20(12):3191-209. PMC: 2630430. DOI: 10.1105/tpc.108.063727. View

14.

Purugganan M, Fuller D . The nature of selection during plant domestication. Nature. 2009; 457(7231):843-8. DOI: 10.1038/nature07895. View

15.

Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N . The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009; 25(16):2078-9. PMC: 2723002. DOI: 10.1093/bioinformatics/btp352. View

16.

Scafaro A, Haynes P, Atwell B . Physiological and molecular changes in Oryza meridionalis Ng., a heat-tolerant species of wild rice. J Exp Bot. 2009; 61(1):191-202. PMC: 2791120. DOI: 10.1093/jxb/erp294. View

17.

Fujino K, Wu J, Sekiguchi H, Ito T, Izawa T, Matsumoto T . Multiple introgression events surrounding the Hd1 flowering-time gene in cultivated rice, Oryza sativa L. Mol Genet Genomics. 2010; 284(2):137-46. DOI: 10.1007/s00438-010-0555-2. View

18.

Valent B, Khang C . Recent advances in rice blast effector research. Curr Opin Plant Biol. 2010; 13(4):434-41. DOI: 10.1016/j.pbi.2010.04.012. View

19.

McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, Kernytsky A . The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 2010; 20(9):1297-303. PMC: 2928508. DOI: 10.1101/gr.107524.110. View

20.

Mizuta Y, Harushima Y, Kurata N . Rice pollen hybrid incompatibility caused by reciprocal gene loss of duplicated genes. Proc Natl Acad Sci U S A. 2010; 107(47):20417-22. PMC: 2996679. DOI: 10.1073/pnas.1003124107. View