Validation and fine characterization of loci involved in environmental adaptation and heterosis

 WP leader: Peter Rogowsky (UMR RDP)
Partners involved: UMR GQE, UMR LEPSE, UMR SADV, UMR IJPB, UMR RDP, Biogemma, Syngenta Seeds.

Context and objectives

Genome wide association studies (WP5) will identify small regions of the genome that contribute to a trait of interest. They will also provide markers to follow beneficial alleles of these genome regions in breeding programs. However, the resolution of the approach differs among genetic regions and some contain up to dozens of genes depending on the local linkage disequilibrium. In addition, as for linkage based QTL mapping, association genetics is a statistical method that only provides correlations but no proof for the implication of particular genes. Neither one sheds any light on the underlying mechanism.

The objectives of WP6 are therefore to (1) provide the tools necessary for the validation of associations and/or fine mapping of QTLs, for the validation of underlying genes, as well as for the creation of de novo variants in these genes and (2) apply these tools to the fine characterization of loci involved in environmental adaptation and heterosis.

WP6 is presently:

• Carrying out the fine analysis of key loci / genomic regions detected by GWA in WP5 or previous projects.
• Creating near isogenic lines with contrasting alleles at the loci of interest, exploiting existing generic introgression resources, to validate allelic series and refine the biological analysis of their effect.
• Providing loss-of-function and/or gain-of-function alleles for genes of these regions by the identification of corresponding mutants or the production of transgenic plants, with the ultimate objective of validating gene functions and investing the usefulness of creating de novo variation.
• Characterizing these materials in detail using phenotyping approaches used in WP5 as well as additional, dedicated analyses.

Deliverables

D6.1: Release to partners of BC5-S1 families ready for extraction of near-isogenic pairs of lines from 750 BC5 selected plants (50 regions x 3 donor-recipient pairs x 5 individuals), 16 regions among 7 BIL populations and NAMxB73 material (M72)

D6.2: Bioinformatics portal for FST sequences of the entire Mutator-induced mutant collection (10 blocks), backcross of requested material (M60)

D6.3: Transgenic plants with reduced or increased expression of genes involved in environmental adaptation/ heterosis (20 constructs, M84).

D6.4: Database with expression profiles in 12 tissues of genotype Fv2 on a genome wide basis (M24)

D6.5.1: Fine position of two major QTL for biomass production under chilling conditions and functional validation results on some of the underlying genes (M96)

D6.5.2: Polymorphic sites associated to F7p mutation (M36) and phenotypic field evaluation of allelic series near-isogenic material in 3 regions contributing to flowering time (M48)

D6.6: Determination of 3 regions of interest for maize adaptation to water deficit, characterization of their effects at the physiological and phenotypic levels, and field evaluation (M96)

D.6.7.1: Molecular, physiological and agronomic analysis of mutants and transgenic plants with decreased and increased expression of genes involved in NUE: 6 transcriptome candidates and up to 6 candidates underlying 2 QTL intervals (M72)

D6.7.2: Detailed phenotypic and molecular description of transgenic loss-of-function plants for 4 transcription factors involved in kernel filling (M96)

D6.8: Phenotypic field evaluation for near-isogenic material in 6 regions contributing to heterosis; estimation of additive (M48), dominant and over-dominant effects of QTL at the metabolic level (M84)