From listmaster animalgenome.org Mon Sep 16 11:33:48 2019
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From: Carine Genet <carine.genetinra.fr>
Postmaster: submission approved by list moderator
To: Members of AnGenMap <angenmapanimalgenome.org>
Subject: Urgent PhD position on Gentics of ruminal microbiota
at INRA France.
Date: Mon, 16 Sep 2019 11:33:48 -0500
Dear All,
Please find below a PhD proposal at INRA France on Genetics of
ruminal microbiota. Please contact Christel for further details:
christel.marie-etancelininra.fr
Have a nice day.
Regards
Carine
------------------------------------------------------------------------
MicroGenOL :
"Understanding the role of the ruminal microbiota in phenotype expression
in Lacaune dairy sheep"
Scientific presentation of the research project
The ruminal microbiota plays a central role in the nutrition of its host,
directly affecting milk production and animal health. Significant
correlations between the ruminal microbiota and milk production or
composition have been found in cows. There are no such studies in sheep,
but milk production and the composition (TB and TP) of sheep's milk are
known to be heritable.
The impact of the host genome on its digestive metagenome is poorly studied
in ruminants. Nevertheless, many researchers report significant inter-
individual variability in the composition of the ruminal microbiota and its
response to a change in the ration, including in the dairy sheep. Beyond
the host genes, the microbiota also depends on horizontal transmission,
especially from mother to young at the time of birth. To our knowledge, no
publication estimates the relative parts of host genetics and maternal
effects on the microbiota.
The pHD work we propose aims to integrate the relationship between genome
and ruminal metagenome of the animal in the modelling of the variability of
production and health phenotypes in ewes. This "multi-omics" approach will
allow us to obtain a detailed characterization of individuals using high
throughput techniques and to propose solutions for a new 3.0 breeding:
- genetic selection of the ewe for a specific rumen bacterial community,
- a potentiation of the phenotype by controlling the ruminal microbiota via
feed
In order to characterize the links between genome and ruminal metagenome,
two questions will be at the basis of the thesis work:
- Is the ruminal microbiota able to shape particular heritable production or
health traits?
- Is the host's genetics capable of shaping a bacterial community?
The research program consists of three phases:
1. The first step will aim to understand the role of the ruminal microbiota
on phenotype expression. In this context, it will be necessary to i) carry
out a bioinformatics analysis of all 16S data together and calculate
indices of diversity and richness of the bacterial community; ii) highlight
the existence of a link between the ruminal microbiota and the traits
measured on animals.
2. The second step will involve studying the influence of the host's
genetics on its bacterial community. This step includes i) the validation
of lines effects (persistence of milk production or somatic cell score) on
the ruminal microbiota in dairy sheep ii) the calculation of the
heritability of bacterial taxon abundances and bacterial richness and
diversity indices, with estimation of the maternal effect in transmission
iii) the identification of QTL via a study of pangenomic associations
between host genome marker SNPs and bacterial taxon abundances (GWAS).
3. The last step will propose to jointly study the influence of the genome
and the ruminal metagenome in the construction of the phenotype. It will be
necessary to i) estimate "metagenomic proximities" between individuals, ii)
assess the variance shares of milk production and health traits related to
genetics (parental matrix or genomic matrix) and linked to microbiota
(metagenomic similarity matrix), iii) schematize the co-involvement of
genomes-metagenomes and the environment in the construction of phenotypes
of interest.
For the realization of this PhD thesis, we will rely on:
- Existing bioinformatics tools: FROGS Package (Find Rapid Otu with Galaxy
Solution) implemented under Galaxy and developed in our laboratory.
- Genotyping data (54 k SNP) of 750 multiparous ewes belonging to 4 genetic
lines: 2 divergent lines (CCS+ and CCS-) on somatic cell count in milk
(marker of udder inflammation), and 2 divergent lines (PERS+ and PERS-) on
milk production persistence,
- Amplicon 16S RNA data already produced in the laboratory (n‡0).
- A database integrating the results of milk recording over the year and at
the time of ruminal sampling (milk composition - TB, TP, fatty acids), and
the results recorded in breeding (milk production, milk emission kinetics,
breast morphology, reproductive performance, live weight, fattening status,
causes of culling) for all 750 ewes.
The last data were collected in 2018. All laboratory samples and analyses
are fully funded, in particular through incentive credits from INRA (PHASE
and GA departments), and the "Investments for the Future" project ANR-11-
INBS-0003.
Co- Supervision :
Annabelle Meynadier - GenPhySE / ENVT
Christel Marie-Etancelin - GenPhySE / INRA
The UMR GenPhySE is attached to the "Animal Genetics" and "Animal
Physiology and Breeding Systems" departments of INRA. The unit's works
constitute a continuum from gene to phenotype and breeding system. They are
organized around 4 scientific axes:
- functional cytogenomics;
- integrative approach to the expression of genomes and metagenomes;
- genetic determinism of complex traits;
- animal populations and breeding systems.
This project is part of the unit's second research axis, and brings
together 2 teams from the UMR:
- the NED team (Nutrition and Digestive Ecosystem) whose objective is to
manage the digestive microbiota to improve the health and digestive
efficiency of animals.
- the GeSPR team (Genetics and Selection of Small Ruminants) whose main
objectives are to better understand the genetic determinism of traits in
small ruminants - including the ruminal microbiota - in order to select
them.
The combination of these 2 teams makes it possible to study the
relationships between the 2 genomes of the host and its microbiota.
Carine GENĂŠT
Chercheur en GĂ©nomique / Genomic Researcher
Carine.Genetinra.fr
INRA-INP UMR1388 GenPhySE
Génétique, Physiologie et Systèmes d'Elevage
Tèl. : +33 (0)5 61 28 57 34
Fax : +33 (0)5 61 28 53 53
Bât.C bureau C207
24, chemin de Borde-Rouge CS52627
31 326 Castanet Tolosan Cedex
France
http://genphyse.toulouse.inra.fr
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