Comparisons of sampling methods for assessing intra and inter-accession genetic diversity in three rice species using genotyping by sequencing

Authors: GOUDA, ARNAUD - Africa Rice Center (AFRICARICE); NDJIONDJOP, MARIE - Africa Rice Center (AFRICARICE); DJEDATIN, GUSTAVE - National Science And Technology University Of Benin; Warburton, Marilyn; GOUNGOULOU, ALPHONSE - Africa Rice Center (AFRICARICE); KPEKI, SÈDJRO - Africa Rice Center (AFRICARICE); N'DIAYE, AMIDOU - University Of Saskatchewan; SEMAGN, KASSA - Africa Rice Center (AFRICARICE)

Submitted to: Scientific Reports
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 7/27/2020
Publication Date: 8/18/2020
Citation: Gouda, A.C., Ndjiondjop, M.N., Djedatin, G., Warburton, M.L., Goungoulou, A., Kpeki, S.B., N'Diaye, A., Semagn, K. 2020. Comparisons of sampling methods for assessing intra and inter-accession genetic diversity in three rice species using genotyping by sequencing. Scientific Reports. 10:13995. https://doi.org/10.1038/s41598-020-70842-0.
DOI: https://doi.org/10.1038/s41598-020-70842-0

Interpretive Summary: International genebanks may contain thousands of important plant accessions (entries), each genetically different from the next. The best way to determine the value of each accession, and put it to use in the best way in a breeding program, is to characterize it using DNA genetic markers. This genetic fingerprint tells researchers how it is unique, and may tell them what useful characteristics they contain. Some accessions are not made up of genetically identical plant seeds; they may be related but each a little different. In order to characterize the entire accession, sampling can be done with 1 or multiple seeds, or a bulk of seeds. This paper shows researchers the cheapest, easiest way to create genetic fingerprints for rice, while retaining the most genetic information possible.

Technical Abstract: To minimize the cost of sample preparation and genotyping, most genebank genomics studies in self-pollinating species are conducted on a single individual to represent an accession, which may not be suitable for assessing the level and distribution of intra- and inter-accession genetic diversity. Here, we compared various population genetics parameters among six DNA (leaf) sampling methods on 90 accessions representing a wild species (O. barthii), landraces (O. glaberrima, O. sativa) and improved varieties derived through interspecific hybridizations. A total of 1,527 DNA samples were genotyped with 46,818 polymorphic single nucleotide polymorphisms (SNPs) using DArTseq. Various statistical analyses were performed on eleven datasets corresponding to 5 plants per accession individually and in a bulk (two sets), 10 plants individually and in a bulk (two sets), all 15 plants individually (one set), and a randomly sampled individual repeated six times (six sets). Overall, we arrived at broadly similar conclusions in terms of SNP polymorphism, heterozygosity, diversity indices, genetic dissimilarity, population structure, and genetic differentiation. Comparisons of dissimilarity matrices computed from eleven datasets revealed very high positive correlations across all 90 accessions (0.925 < r < 0.998), supporting the possibility of using any of the sampling methods in large-scale rice germplasm curation and characterization. There were, however, a few exceptions, including low correlations between some pair of datasets in O. glaberrima. Detailed results of each sampling method, the concordance in their outputs, and the technical and cost implications of each method were discussed.