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Development of a SNP genotyping panel for detecting polymorphisms in Oryza glaberrima/O. sativa interspecific crosses

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Oryza glaberrima accessions harbor genes for tolerance to abiotic stresses such as mineral deficiency in problem soils. This genetic potential could be exploited in interspecific crosses with Oryza sativa, as in the case of the ‘New Rice for Africa’ (NERICA) varieties; however, to attain this goal it would be desirable to develop a high-throughput marker system to specifically detect O. glaberrima introgressions in an O. sativa background. Therefore, a single nucleotide polymorphism (SNP) genotyping analysis of an O. glaberrima accession (CG14) with two O. sativa lines (WAB56-104 and WAB181-18) was performed on a genome-wide basis. Comparison of CG14 and the WAB lines resulted in a set of 9,523 polymorphic SNPs which would be suitable to detect O. glaberrima introgressions in upland NERICAs. In addition, a set of 1,540 polymorphic SNPs between O. glaberrima versus O. sativa was identified. A subset of SNPs which were evenly distributed in the genome was then used to design a flexible and cost-effective SNP genotyping panel using the Competitive Allele-Specific PCR technology (KASP). This SNP genotyping panel consists of 2,015 SNPs successfully converted into KASP markers, providing 745 polymorphic SNPs for the parents O. glaberrima CG14/O. sativa WAB56-104 (upland NERICA), and 752 for O. glaberrima TOG5681/O. sativa IR64 (lowland NERICA). KASP markers were successfully validated by mapping O. glaberrima introgressions in NERICA-derived breeding lines. This new SNP genotyping panel will be useful in modern breeding applications such as QTL mapping and/or marker-assisted selection.

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We thank Dr. Yoshimichi Fukuta (JIRCAS, Japan) for providing his SSR genotyping data on NERICA varieties. Likewise, we thank Taro Matsuda for his technical assistance.

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Correspondence to Matthias Wissuwa.

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Online resource 1–Table S1. The complete list of 44 K SNP genotyping data. A SNP genotyping analysis of O. glaberrima (CG14) and O. sativa (WAB56-104, WAB181-18, IR74) was performed on a genome-wide basis using the 44 K SNP Affymetrix genotyping array. (XLS 15683 kb)


Online resource 2–Fig. S1. Distribution of polymorphic SNPs between O. glaberrima CG14 and six O. sativa accessions. (DOC 55 kb)


Online resource 3–Table S2. The complete list of SNP–KASP markers. A set of selected SNPs were successfully converted into KASP markers. The genotyping data for the parents of upland and lowland NERICAs (O. glaberrima and O. sativa) is presented. (XLS 443 kb)


Online resource 4–Table S3. KASP data for N10W3/4 lines.The N10W3 and N10W4 are two BC1F4 sister lines derived from a NERICA10 × WAB56-104 backcross used for mapping O. glaberrima introgressions. (XLSX 220 kb)


Online resource 5–Table S4. Flanking region for each SNP–KASP marker. The physical position and the flanking region of each KASP marker is provided. The SNP is represented as [x/y], where x and y indicate the allele. (XLSX 180 kb)

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Pariasca-Tanaka, J., Lorieux, M., He, C. et al. Development of a SNP genotyping panel for detecting polymorphisms in Oryza glaberrima/O. sativa interspecific crosses. Euphytica 201, 67–78 (2015).

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