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Genome-wide SNP genotyping of DNA pools identifies original landraces to enrich maize breeding genepools

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 breeding pools. 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 the diversity of this collection at genome-wide scale level with that of a panel of 336 inbred lines. Our new approach: (i) gives accurate allelic frequencies estimation that are reproducible across laboratories, (ii) protects both against false detection of allele presence within landraces and against ascertainment bias. Modified Roger's genetic Distance estimated from 23412 SNP and 17 SSR on same DNA pool are highly correlated, which validates our approach. Accordingly, structuration analysis based on SNP gives consistent results with SSR for higher levels of structuration but gives a slightly different pictures for more advanced structuration levels, suggesting that SNP and SSR could capture differently recent evolution. Gene diversity of landraces varies strongly along the genome and according to 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 pools as Reid Yellow Dent or Lancaster Surecrop, some other have no related inbred lines and seem to have poorly contributed. We identified limited diversity loss or selective sweep between landraces and inbred lines, excepted in centromeric regions. For these regions, original landraces could be interesting to enlarge genetic diversity of modern breeding pools
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https://hal.inrae.fr/hal-03368726
Contributor : Stéphane Nicolas Connect in order to contact the contributor
Submitted on : Wednesday, October 6, 2021 - 10:12:18 PM
Last modification on : Friday, August 5, 2022 - 2:38:10 PM

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  • HAL Id : hal-03368726, version 1

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Stephane Nicolas, Mariangela Arca, Tristan Mary Huard, Marie-Christine Le Paslier, Cyril Bauland, et al.. Genome-wide SNP genotyping of DNA pools identifies original landraces to enrich maize breeding genepools. Harlan International Symposium : Harlan III, Jun 2021, Montpellier, France. ⟨hal-03368726⟩

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