GENM - Génomique

Cattle and sheep milk fine components analysis and genotyping program to detect and use QTL or major genes linked to milk content. – LactoScan

Submission summary

This project aims at determining the main genetic and environmental factors determining fine milk composition in fat and protein. It includes 3 tasks but is a part of a larger programme with six tasks, three of them being supported by non-ANR fundings : (1) adapt Mid Infra Red (MIR) spectrometers of the different milk analysis laboratories to export spectra, develop a dedicated data base ; (2) develop calibration equations to predict fatty acid composition of milk in the three dairy species through MIR and chromatography data, from samples collected in four INRA farms; (3=task1) develop a reference method for protein measurement and derive calibration equations by the analysis of both reference and MIR data ; (4=task2) collect MIR spectra, milk and blood samples, and diet and management information from 12,000 cows and 3,000 ewes, as well as complementary information from the national database ; predict fatty acid and protein concentration from MIR spectra ; (5=task3) genotype a part of these samples with a SNP chip and perform QTL fine mapping, determine the effect of management and feeding policies on fatty acids and protein profiles in milk. (6) develop management and feeding strategies for general recommendation. Steps (3), (4) and (5) are included in this Genomic project and are denoted TASK1, TASK2, and TASK3, respectively. Specific aims of TASK1 is first to establish a detailed qualitative and quantitative profile of the 12 main milk proteins: caseins, alpha-lactalbumin, beta-lactoglobulin, lactoferrin, lactoperoxydase, using highly resolvent reference steadfast (RP-HPLC) and innovative (UPLC) techniques combined with Mass Spectrometry (MS). The challenge will be to identify the known (and eventually unknown) genetic variants and different isoforms and to determine their relative proportions. The second aim will be to derive from the detailed phenotype descriptions a calibration equations allowing the prediction of the milk protein fraction composition on a large number of milk samples by MIR.

TASK2 aims at collecting all the samples and informations required by the project in a large number of commercial farms, in cattle as well as in sheep. 12,000 Holstein, Normande and Montbéliarde cows and 3,000 Lacaune ewes are targeted, based on prior information in the national data base. In cattle, herds are defined according to their size, their geographic concentration around labs participating to the project, their breeds, and their genetic diversity. Four kinds of information are collected: (1) three milk samples per lactation, (2) MIR spectra from these samples, (3) blood samples from the corresponding cows, for DNA extraction, (4) diet and management information for a good interpretation of the results.

TASK3 is the genotyping step. About two thirds of the blood samples are selected for DNA extraction and genotyping, on the basis of MIR results. Depending on the cost of the chips in 2010, two options are possible. The most conservative is proposed as a minimum. A dedicated 1536-SNP chip will be developed to target all regions of interest, defined on the basis of external knowledge (results from Le Pin QTL experiment, Sarde data, other literature data, QTL known to affect total fat or protein). The chip will be completed by additional markers from the remaining part of the genome at a lower density. Data will be analysed by combining linkage and linkage disequilibrium. The effect of all environmental and diet factors will be estimated.

Project coordinator

Monsieur Didier BOICHARD (INSTITUT NATIONAL DE LA RECHERCHE AGRONOMIQUE - CENTRE DE RECHERCHE DE JOUY-EN-JOSAS)

The author of this summary is the project coordinator, who is responsible for the content of this summary. The ANR declines any responsibility as for its contents.

Partner

INSTITUT DE L'ELEVAGE
INSTITUT NATIONAL DE LA RECHERCHE AGRONOMIQUE - CENTRE DE RECHERCHE DE JOUY-EN-JOSAS
INSTITUT NATIONAL DE LA RECHERCHE AGRONOMIQUE - CENTRE DE RECHERCHE DE JOUY-EN-JOSAS

Help of the ANR 664,544 euros
Beginning and duration of the scientific project: - 36 Months

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