Title: Development of a SNP diversity panel in chicken

Project manager: Dr. S. Weigend (FLI-NG)

Project partners: FLI-NG, TUM-TZ, UGÖ-TZ

Objective:
Development of a diversity panel in chicken for population genomic analyses.

Summary:
In project R2 DNA samples from 100 genetically diverse breeds of chickens are collected for genotyping in the technology platform T2 of the Synbreed cluster with a 60k chicken SNP array. The resulting data are a vital resource for population genomic analyses in the Synbreed A4 project. At the same time data will be used for high-resolution analysis of phylogenetic relationships between the populations studied. Outcome of these analyses will be compared to results obtained from microsatellite data. The chicken populations will include commercial breeding lines as well as a selection of various local breeds from different continents and management systems. Part of the samples will be taken from the chicken DNA bank established at the Institute of Farm Animal Genetics (FLI) in Neustadt-Mariensee. These populations have already been genotyped at 29 microsatellite loci. We will use populations differing in the degree of polymorphism (high and low polymorphic populations) and genetic relationship (unrelated and closely related populations), respectively. About 2 / 3 of the population samples will be newly collected. For those populations we will also collect individual phenotypic information in addition to DNA samples. A standardized protocol for phenotypic characterization of genetic diversity in chickens will be developed, comprising both discrete and continuous morphological traits. Multivariate methods of data analysis will identify the most informative combination of genetic and phenotypic markers that can be used in future biodiversity studies.