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Whole-genome modeling accurately predicts quantitative traits, as revealed in plants.

By Laurent Gentzbittel, Cécile Ben, Mélanie Mazurier, Min-Gyoung Shin, Martin Triska, Martina Rickauer, Yuri Nikolsky, Paul Marjoram, Sergey Nuzhdin, Tatiana V. Tatarinova

Posted 31 Oct 2015
bioRxiv DOI: 10.1101/030395 (published DOI: 10.1186/s13059-019-1697-0)

Many adaptive events in natural populations, as well as response to artificial selection, are caused by polygenic action. Under selective pressure, the adaptive traits can quickly respond via small allele frequency shifts spread across numerous loci. We hypothesize that a large proportion of current phenotypic variation between individuals may be best explained by population admixture. We thus consider the complete, genome-wide universe of genetic variability, spread across several ancestral populations originally separated. We experimentally confirmed this hypothesis by pre- dicting the differences in quantitative disease resistance levels among accessions in the wild legume Medicago truncatula. We discovered also that variation in genome admixture proportion explains most of phenotypic variation for several quantitative functional traits, but not for symbiotic nitro- gen fixation. We shown that positive selection at the species level might not explain current, rapid adaptation. These findings prove the infinitesimal model as a mechanism for adaptation of quantitative phenotypes. Our study produced the first evidence that the whole-genome modeling of DNA variants is the best approach to describe an inherited quantitative trait in a higher eukaryote organism and proved the high potential of admixture-based analyses. This insight contribute to the understanding of polygenic adaptation, and can accelerate plant and animal breeding, and biomedicine research programs.

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