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Title: Genetic variation and population structure of Oryza glaberrima and development of a mini-core collection using DArTseq

Author
item NDJIONDJOP, MARIE-NOELLE - Africa Rice Center (AFRICARICE)
item SEMAGN, KASSA - University Of Alberta
item GOUDA, ARNAUD - Africa Rice Center (AFRICARICE)
item KPEKI, SEDJRO - Africa Rice Center (AFRICARICE)
item DRO, TIA - Africa Rice Center (AFRICARICE)
item SOW, MOUNIROU - Africa Rice Center (AFRICARICE)
item GOUNGOULOU, ALPHONSE - Africa Rice Center (AFRICARICE)
item SIE, MOUSSA - Africa Rice Center (AFRICARICE)
item PERRIER, XAVIER - Cirad, France
item GHESQUIERE, ALAIN - Umr - Bgpi, Biologie Et Génétique Des Interactions Plante-parasite
item Warburton, Marilyn

Submitted to: Frontiers in Plant Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 9/25/2017
Publication Date: 10/17/2017
Citation: Ndjiondjop, M., Semagn, K., Gouda, A.C., Kpeki, S.B., Dro, T., Sow, M., Goungoulou, A., Sie, M., Perrier, X., Ghesquiere, A., Warburton, M.L. 2017. Genetic variation and population structure of Oryza glaberrima and development of a mini-core collection using DArTseq. Frontiers in Plant Science. 8(1748):1-19. https://doi.org/10.3389/fpls.2017.01748.
DOI: https://doi.org/10.3389/fpls.2017.01748

Interpretive Summary: Rice, along with maize and wheat, provide the majority of food calories to people around the world. The conservation of genetic sequence diversity present in the many different improved varieties, farmer’s varieties, and wild and weedy relatives of rice, can be used to find new gene variants to improve any trait of interest. These varieties are stored in different gene banks around the world. The AfricaRice gene bank has 22,000 registered rice samples. Of these, the varieties belonging to the species Oryza glaberrima represent one of the two cultivated species grown in Africa. By genetically fingerprinting all the O. glaberrima varieties in the collection, gene bank curators can ensure there are no duplicated or incorrectly classified varieties; that the varieties are being maintained in their original, pure form; and that there are no regions in Africa from which varieties have not been collected (gaps). In addition, curators can take the 2,179 O. glaberrima varieties in the gene bank and choose a smaller subset of varieties that represent the total genetic variation of the collection. Rice breeders can then look at this much smaller, representative subset to find any trait they are interested in, rather than look at the entire collection. Here, subsets of 1,330 and 350 accessions were chosen using molecular markers to represent a core and mini-core collection, respectively. The core and mini-core sets captured 97-99% of the genetic diversity present in the whole O. glaberrima collection available at the AfricaRice gene bank.

Technical Abstract: The sequence variation present in accessions conserved in gene banks can best be used in plant improvement when it is properly characterized and published. Using low cost and high density single nucleotide polymorphism (SNP) assays, the genetic diversity, population structure, and relatedness between pairs of accessions can be quickly assessed. This information is relevant for different purposes, including creating core and mini-core sets that represent the maximum possible genetic variation contained in the whole collection. Here, we studied the genetic variation and population structure of 2,179 Oryza glaberrima Steud. accessions conserved at the AfricaRice gene bank using 27,560 DArTseq-based SNPs. Only 14% (3,834 of 27,560) of the SNPs were polymorphic across the 2,179 accessions, which is much lower than diversity reported in other Oryza species. Genetic distance between pairs of accessions varied from 0.005 to 0.306, with 1.5% of the pairs nearly identical, 8.0% of the pairs similar, 78.1% of the pairs moderately distant, and 12.5% of the pairs very distant. The number of redundant accessions that contribute little or no new genetic variation to the O. glaberrima collection was very low. Using the maximum length sub-tree method, we propose a subset of 1,330 and 350 accessions to represent a core and mini-core collection, respectively. The core and mini-core sets accounted for ~ 61 and 16%, respectively, of the whole collection, and captured 97-99% of the SNP polymorphism and nearly all allele and genotype frequencies observed in the whole O. glaberrima collection available at the AfricaRice gene bank. Cluster, principal component and model-based population structure analyses all divided the 2,179 accessions into five groups, based roughly on country of origin but less so on ecology. The first, third and fourth groups consisted of accessions primarily from Liberia, Nigeria, and Mali, respectively; the second group consisted primarily of accessions from Togo and Nigeria; and the fifth and smallest group was a mixture of accessions from multiple countries. Analysis of molecular variance showed between 10.8- 28.9% of the variation among groups with the remaining 71.1-89.2% attributable to differences within groups.