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Conference papers

DNA pooling for evaluating originality of the landraces

Abstract : Maize landraces germplasm have a very large genetic diversity that is still poorly characterized and exploited in plant breeding programs. We studied the effect of both human selection and environmental adaptation on genome-wide diversity of landraces with a focus on landraces-hybrid transition in order to identify interesting source of genetic diversity to enlarge modern inbred lines pool. We developed a high-throughput, cheap and labor saving DNA pooling approach based on 50K SNP maize Illumina array and estimated thereby allelic frequencies of 23412 SNP in 156 landraces representing worldwide maize diversity. We compared diversity at both global and genome-wide scale level with a diversity panel of 336 inbred lines. Our new approach: (i) gives accurate allelic frequencies estimation that are reproducible across laboratories, (ii) protects both against detection of false allele presence within landraces population and against ascertainment bias. Modified Roger's genetic Distance estimated from 23412 SNP and 17 SSR on same DNA pool are highly correlated validating our approach. Accordingly, structuration analysis based on SNP give consistent results with SSR for highly level of structuration but give a slightly different pictures for more advanced structuration level suggesting that SNP and SSR could capture differently recent evolution. Gene diversity varies strongly globally and along the genome between the landraces and according to their geographic origins. We identified 376 SNP under diversifying selection unraveling a selective footprints in Tga1/Su1 regions. While some maize landraces were closely related to several inbred lines and strongly contributed to modern breeding pool as Reid Yellow Dent or Lancaster Surecrop, some other have no related inbred lines and seems to have poorly contributed. Surprisingly, we identified few diversity loss or selective sweep between landraces and inbred lines excepted in centromeric regions. Theses landraces and genomic regions could be interesting to enlarge genetic diversity of modern breeding pool.
Mots-clés : DNA landraces
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Conference papers
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https://hal.inrae.fr/hal-02786301
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Submitted on : Thursday, June 4, 2020 - 11:53:12 PM
Last modification on : Friday, August 5, 2022 - 2:38:10 PM

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  • HAL Id : hal-02786301, version 1
  • PRODINRA : 481798

Citation

Stephane S. Nicolas, Mariangela Arca, Tristan Mary-Huard, Brigitte Gouesnard, Marie-Christine Le Paslier, et al.. DNA pooling for evaluating originality of the landraces. 1. German-French Maize Breeders School, May 2017, Hohenheim, Germany. ⟨hal-02786301⟩

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