Development of species diagnostic SNP markers for quality control genotyping in four rice (Oryza L.) species

Marie Noelle Ndjiondjop, Kassa Semagn, Jianwei Zhang, Arnaud Comlan Gouda, Sèdjro Bienvenu Kpeki, Alphonse Goungoulou, Peterson Wambugu, Khady Nani Dramé, Isaac Kofi Bimpong, Dule Zhao

    Research output: Contribution to journalArticlepeer-review

    12 Scopus citations


    Species misclassification (misidentification) and handling errors have been frequently reported in various plant species conserved at diverse gene banks, which could restrict use of germplasm for correct purpose. The objectives of the present study were to (i) determine the extent of genotyping error (reproducibility) on DArTseq-based single-nucleotide polymorphisms (SNPs); (ii) determine the proportion of misclassified accessions across 3134 samples representing three African rice species complex (Oryza glaberrima, O. barthii, and O. longistaminata) and an Asian rice (O. sativa), which are conserved at the AfricaRice gene bank; and (iii) develop species- and sub-species (ecotype)-specific diagnostic SNP markers for rapid and low-cost quality control (QC) analysis. Genotyping error estimated from 15 accessions, each replicated from 2 to 16 times, varied from 0.2 to 3.1%, with an overall average of 0.8%. Using a total of 3134 accessions genotyped with 31,739 SNPs, the proportion of misclassified samples was 3.1% (97 of the 3134 accessions). Excluding the 97 misclassified accessions, we identified a total of 332 diagnostic SNPs that clearly discriminated the three indigenous African species complex from Asian rice (156 SNPs), O. longistaminata accessions from both O. barthii and O. glaberrima (131 SNPs), and O. sativa spp. indica from O. sativa spp. japonica (45 SNPs). Using chromosomal position, minor allele frequency, and polymorphic information content as selection criteria, we recommended a subset of 24 to 36 of the 332 diagnostic SNPs for routine QC genotyping, which would be highly useful in determining the genetic identity of each species and correct human errors during routine gene bank operations.

    Original languageEnglish (US)
    Article number131
    JournalMolecular Breeding
    Issue number11
    StatePublished - Nov 1 2018


    • African rice
    • Asian rice
    • Cultivated rice
    • DArTseq
    • Genotyping by sequencing
    • Wild rice

    ASJC Scopus subject areas

    • Biotechnology
    • Molecular Biology
    • Agronomy and Crop Science
    • Genetics
    • Plant Science


    Dive into the research topics of 'Development of species diagnostic SNP markers for quality control genotyping in four rice (Oryza L.) species'. Together they form a unique fingerprint.

    Cite this