An extensive analysis of the African rice genetic diversity through a global genotyping

Autor: Sophie Chéron, Yves Vigouroux, Julie Orjuela, Mathias Lorieux, Kayode Sanni, Hélène Adam, Harold Chrestin, Alain Ghesquière, François Sabot
Přispěvatelé: Diversité, adaptation, développement des plantes (UMR DIADE), Institut de Recherche pour le Développement (IRD [France-Sud])-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)
Rok vydání: 2014
Předmět:
0106 biological sciences
History
DNA
Plant
Genotype
Reveals adaptation
[SDV]Life Sciences [q-bio]
Resistance
Plant genetics
Population
Oryza sativa
Biology
Oryza glaberrima
Population structure
Polymorphism
Single Nucleotide
01 natural sciences
Domestication
03 medical and health sciences
Origin
Genetic variation
Genetics
Plant breeding
education
Genotyping
030304 developmental biology
[SDV.GEN]Life Sciences [q-bio]/Genetics
0303 health sciences
Genetic diversity
education.field_of_study
Severe bottleneck
Geography
Resistance (ecology)
business.industry
Glaberrima
Genetic Variation
food and beverages
Oryza
Sequence Analysis
DNA
General Medicine
Yellow mottle virus
biology.organism_classification
Biotechnology
Genetics
Population
Evolutionary biology
Africa
Hybridization
Genetic
business
Agronomy and Crop Science
010606 plant biology & botany
Zdroj: TAG Theoretical and Applied Genetics
TAG Theoretical and Applied Genetics, Springer Verlag, 2014, 127 (10), pp.2211-2223. ⟨10.1007/s00122-014-2374-z⟩
ISSN: 1432-2242
0040-5752
DOI: 10.1007/s00122-014-2374-z
Popis: We present here the first curated collection of wild and cultivated African rice species. For that, we designed specific SNPs and were able to structure these very low diverse species. Oryza glaberrima, the cultivated African rice, is endemic from Africa. This species and its direct ancestor, O. barthii, are valuable tool for improvement of Asian rice O. sativa in terms of abiotic and biotic stress resistance. However, only a few limited studies about the genetic diversity of these species were performed. In the present paper, and for the first time at such extend, we genotyped 279 O. glaberrima, selected both for their impact in current breeding and for their geographical distribution, and 101 O. barthii, chosen based on their geographic origin, using a set of 235 SNPs specifically designed for African rice diversity. Using those data, we were able to structure the individuals from our sample in three populations for O. barthii, related to geography, and two populations in O. glaberrima; these two last populations cannot be linked however to any currently phenotyped trait. Moreover, we were also able to identify misclassification in O. glaberrima as well as in O. barthii and identified new form of O. sativa from the set of African varieties.
Databáze: OpenAIRE
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