Mining genetic diversity for tomorrow’s agriculture

Genetic diversity is the key ingredient fueling gains during plant breeding programs. Thus, understanding the structure of a germplasm’s genetic diversity as well as the factors shaping it pave the way for crop improvement. During my thesis, I utilized quantitative modeling and bioinformatic approaches to study both meiotic recombination, a factor driving genome reshuffling, and the genetic diversity of two important crops, tomato and peanut. For meiotic recombination, individual genomic/epigenomic features have weak predictive power regarding the distribution of crossovers in Arabidopsis thaliana. Instead, a summarized epigenetic status, referring to 10 chromatin states, is able to reveal the associated landscape rather well. Furthermore, I found that intermediate levels of single nucleotide polymorphisms (SNPs) between homologs leads to more crossovers compared to the case of near identical sequences, and that intergenic regions of size less than 1.5 kb tend to suppress crossovers. Taken together, I integrated these effects into a quantitative model that can predict recombination landscapes and that reproduces much of the variation seen in the experimental crossover data. Moving on to the cultivated tomato, one of its most destructive diseases is Bacterial wilt (BW). I used the whole genome sequence data of six BW resistant and nine BW susceptible lines to identify polymorphisms specific to resistant lines. Among resistant-specific polymorphisms affecting 385 genes, the marker Bwr3.2dCAPS located in the Asc (Solyc03g114600.4.1) was shown to be significantly associated with the BW resistance but nevertheless it does not fully explain the resistance phenotype. Lastly, I assessed the genetic diversity of cultivated peanuts in Taiwan by the restriction site associated DNA (RAD) approach using 31 accessions. My results indicate that worldwide accessions have greater genetic diversity than local accessions, suggesting that novel genetic resources should be introduced into the present breeding programs for enhancing the genetic diversity. These successive investigations, motivated respectively by fundamental biology and by applied breeding science, provide new insights that can help future strategies for crop improvement.

Jury

Beth Rowan, Cécile Fairhead, Martin Howard, Mathias Lorieux and Piotr Ziółkowski.

Thesis direction

Matthieu Falque and Olivier Martin