LANDSREC The high-resolution landscapes in rice meiotic recombination

To better understand the epigenetic and genetic factors involved in the distribution of meiotic cross-overs in order to establish a predictive tool for their occurrence for genetic analyses and plant breeding

Date de début de projet

01/01/2022

Date de fin du projet

31/12/2025

Objectives

.LANDSREC will establish the distribution of double-strand breaks (DSBs) and meiotic cross-overs (COs) in the model cereal crop genome, rice, and will compare them with high-resolution chromosomal landscapes (epigenetic marks, sequence polymorphism and structural variations) in order to:

i. better understand the factors involved in the realization of DSBs

ii. Determine the influence of sequence polymorphism and structural variations on DSB repair as CO and

iii. establish a predictive model for the occurrence of a CO in a given chromosomal region when the sequence of both parents is known and visualize the probability of occurrence on a genome browser

Location

  • WP1 : Epigenomics of chromosomes at prophase of meiosis, using purified male meiocytes (IPS2, AGAP) (IR64, Azucena, IR64/Azucena hybrid, meiotic vs. somatic)
  • WP2 : High resolution DSB landscape by sequencing SPO11-linked oligonucleotides in IR64/Azucena floral tissues (AGAP, IPS2)
  • WP3: High resolution CO landscape by sequence analysis of 2,000 F2 derived from the F1 hybrid IR64/Azucena. Relationship to nucleotide and structural divergences between the two parental genomes for establishing the model. Test of the model in a hyper-recombinant population of the same cross and Nested Association Mapping (NAM) populations of other crosses. (DIADE, AGAP)
  • WP4: Integration of genomic data and development of a visualization tool for CO probability in the Rice Genome Hub (AGAP, DIADE)

Description

LANDSREC combines expertise in cell biology (AGAP), epigenomics (IPS2), genetics (DIADE, AGAP) and bioinformatics (AGAP, DIADE) and is organized into 4 work packages (WP):

  • WP1 : Epigénomique des chromosomes en prophase de méiose chez les méiocytes mâles purifiés (IPS2, AGAP) (IR64, Azucena, hybride IR64/Azucena, meiotique vs. somatique)WP2 :  Paysage des CDB à haute résolution par séquençage des oligonucléotides liés à SPO11 (AGAP, IPS2)
  • WP3 :  Paysage des CO à haute résolution par analyse des séquences de 2000 F2. Mise en relation avec le polymorphisme et variations structurales entre parents pour l’établissement du modèle. Test du modèle dans une population hyper-recombinante du même croisement et des populations NAM d’autres croisements. (DIADE, AGAP)
  • WP4 :  Intégration des données génomiques et développement d’un outil de visualisation de la probabilité de CO dans le rice genome hub (AGAP, DIADE)

Partnership

CIRAD, IRD, UPS

Team

Genetics and variety innovation (GIV)

Fundings

ANR, 590 K€

Meiosis, recombination, double strand breaks, cross-overs, prediction