Project Number: 3635-31320-008-09
Project Type: Specific Cooperative Agreement

Start Date: Aug 15, 2005
End Date: Apr 30, 2008

Objective:
1. Simultaneously validate and determine the allele frequency of ~3,000 cnSNPs equally spaced throughout the chicken genome by genotyping parents of specific resource populations (12 individuals), and 40 birds from each of 36 elite commercial breeding populations (both broilers and layers). 2. Genotype the same ~3,000 cnSNPs on the East Lansing (EL, 2 parents plus 88 progeny) and Wageningen (WAU, two families with 4 parents plus 96 progeny) reference panels to map informative markers, and help confirm, enhance, or resolve discrepancies between the genetic map and the draft genome sequence. 3. Simultaneously validate and determine the extent of linkage disequilibrium (LD) in commercial chicken lines by genotyping ~1,500 SNPs at varying distance across 6 regions on 960 chickens in 10 different pedigreed populations.

Approach:
Two large sets of SNPs will be genotyped. In the first set, which is designed to address whether cnSNPs are valid, segregating in resource population, and determine the allele frequency in elite commercial lines, we will genotype ~3,000 cnSNPs on ~1,600 individuals (36 lines x 40 individuals each = 1440 samples, the parents and progeny of the EL and WAU reference panels, and parents of various resource populations). Markers that have two alleles will be declared valid. Allele frequencies within and across lines will be calculated. Informative SNPs in the EL and WAU reference panels will be mapped and compared to the locations in the draft genome sequence. The second set of SNPs is designed to determine the extent of LD in commercial chicken lines. Focusing on 6 regions, 250 markers at varying distance will be designed for each region. These SNPs will then be genotyped on 960 individuals of a population designed to determine LD. The resulting datasets will allow us to mine much information. In this proposal, we will focus on two areas. First, traceability will be evaluated as to how many generations an individual can be traced back to the parental population, which addresses an area of need by the industry. Second, the marker allele will help to refine the GMAS simulations and determine the applicability of molecular markers in poultry breeding.