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PhD theses defended at IPS2 during summer 2022


Genomic and epigenomic immunity in common bean (Phaseolus vulgaris): lessons learned from chromosome scale genome assemblies

Keywords: Phaseolus vulgaris, genome assembly, resistance genes

Common bean is the most consumed grain legume in the world for human feeding. Two available genome assemblies allowed to identify RNA silencing genes in bean, some of which are induced after infection by Colletotrichum lindemuthianum, and to perform a transcriptomic analysis revealing the importance of the defense proteins PR10/Bet-V1 after infection. Furthermore, to study the evolution of repeated sequences (NLR and satellite DNA), we generated highly contiguous assemblies for two genotypes using PacBio HiFi sequencing and Hi-C scaffolding. Within the NLR clusters, important structural variations were observed between genotypes, as well as methylation polymorphism for NLRs in the Co-2 resistance cluster. Finally, we identified a transposable element (TE) inserted in the candidate NLR gene encoding for a resistance gene to BCMV, and likely corresponding to a recent insertion.

Defense date: July 21, 2022

Supervisors: V. GEFFROY and A. GRATIAS-WEILL

Yu-Ming HSU

Mining genetic diversity for tomorrow’s agriculture

Key words: biostatistics, computation, statistical inference, plant breeding

Genetic diversity is the key ingredient fueling gains in plant breeding. Thus, understanding the structure of a germplasm’s genetic diversity and the factors shaping it pave the way for crop improvement. We used quantitative modeling and bioinformatic approaches to study meiotic recombination and the genetic diversity of two important crops, tomato and peanut. For meiotic recombination, a summarized epigenetic status, the levels of single nucleotide polymorphisms (SNPs), and the size of intergenic regions, were integrated into a quantitative model that reproduces much of the variation seen in the experimental crossover data. We also quantified the genetic diversity of Taiwanese peanut accessions, and identified a candidate gene contributing to the resistance against bacterial wilt in tomato. These investigations in fundamental biology and applied breeding science provide new insights that can help future strategies for crop improvement.

Defense date: September 7, 2022

Supervisors: M. FALQUE and O. MARTIN


Genetic and -omic analysis of nectary development: identification of key traits for improvement of foraging activity

Keywords: Cucumis melo L., flower, nectar, nectary, pollinators

Nectar is the key reward that plants use to outsource pollination services and ensure reproductive success. The nectar-secreting organs, the nectaries, play the central role in maximizing seed set, however, the molecular mechanisms underlying their development remain understudied. The thesis project allowed improving our understanding of nectary development and nectar secretion in relation with pollinator foraging, key traits that impact fruit yield, its stability and food availability for bees. First, accessions of melon that differ in nectary development, nectar secretion and their effects on bee visitation, were phenotypically characterized. Second, the gene networks controlling nectary development in unisexual flowers were studied. Third, the impact of the genetic concepts identified on the foraging activity and behavior of bees was validated. The challenge is now to link the genetic model to nectar-related traits to enhance crop-pollinator interactions.

Defense date: September 16, 2022

Supervisors: A. BENDAHMANE and C. DOGIMONT

PhD theses defended at IPS2 during summer 2022