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SNP genotyping and characterization of pistil traits revealing a distinct phylogenetic relationship among the species of Oryza

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Abstract

The genomic structure of Oryza species is informative to widen the genetic base and to design strategies for more efficient rice improvement programs. 384-plex GoldenGate SNP genotyping of 48 accessions of cultivated and wild species were used to determine the population structure and to explore the variation in stigma and style length of Oryza species. More than 98 % of the SNPs were amplified in O. sativa subspecies indica and japonica whereas, among the AA genome wild species, O. longistaminata and O. meridionalis had the lowest amplification of 80 and 72 %, respectively. Population structure analysis grouped the 48 accessions into six subpopulations: I. O. sativa subspecies indica, II. O. sativa subspecies japonica, III. O. nivara, IV. O. sativa complex, V. O. officinalis complex, and VI. O. meyeriana and O. ridleyi complex. Phylogentic analysis based on evolutionary dissimilarities supported most of the groupings done in the bayesian cluster analysis. A wide range of variability was present for pistil characteristics in Oryza species. Among the wild species in the AA genome, O. longistaminata has significantly longer stigma, style, and total pistil length than the remaining Oryza species. We identified five SNP loci on chromosomes 3, 4, 7, and 10 that have shown significant association with stigma length, style length, and stigma plus style length, and explained 17–24 % of the phenotypic variation. The present study is useful to unravel the mechanisms governing natural genetic variation for stigma length which will be useful in improving out-crossing rate in rice for increased hybrid seed production.

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Acknowledgments

We would like to thank several anonymous reviewers for a critical review of this manuscript and for their valuable comments. We thank Bill Hardy, Senior Science Editor of IRRI, for editing the manuscript.

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Authors and Affiliations

  1. Plant Breeding, Genetics, and Biotechnology Division, International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines

    Balram Marathi, Joie Ramos, Sherry L. Hechanova, Rowena H. Oane & Kshirod K. Jena

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  1. Balram Marathi
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  2. Joie Ramos
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Correspondence to Kshirod K. Jena.

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Marathi, B., Ramos, J., Hechanova, S.L. et al. SNP genotyping and characterization of pistil traits revealing a distinct phylogenetic relationship among the species of Oryza . Euphytica 201, 131–148 (2015). https://doi.org/10.1007/s10681-014-1213-2

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