Updates on genomic evaluation software (gebv). - CGIL

<strong>Updates</strong> on genomic evaluation software (gebv)
Sargolzaei, M. 12 , Schenkel, F. 2 and Chesnais, J. 1
1 L'Alliance Boviteq, Saint-Hyacinthe, QC, Canada
2 University of Guelph, Centre for Genetic Improvement of Livestock, Guelph, ON, Canada
The gebv software was updated to improve its functionality, including the use of imputed genotypes.
The following updates were made:
Major improvements:
• Partial genotypes, which might be more common with imputed genotypes, can now be handled by
gebv;
• Significant improvement in memory usage for creating G matrix;
• Parentage test was added, including report on pedigree errors, sex errors, possible parent match
for animals with missing parents or ungenotyped parent, and identical genotypes;
• Report on the relatedness of an animal with the estimation group (average pedigree-based
relationship) and also checking if the parents and grandparents of an animal belong to estimation
group. This should be an important additional information, since the accuracy of GEBV is, in
some degree, a function of relationship of the animal with the estimation group;
• The memory allocation when analysing very dense SNP panel (800k) was optimized.
• Other utility programs, such as imputation (fimpute) and linkage disequilibrium (snppld)
programs are now part of gebv software package. The fimpute software imputes genotypes using
a pedigree-based algorithm. The snppld software calculates pairwise LD (r2 and D' measures) for
syntenic and nonsyntenic SNP and outputs the detailed statistics and draws LD graphs. This
program can be used to find SNP pairs in very high LD and to spot misplaced SNP. All utility
programs read the same input format.
Other improvements:
• Faster G calculation;
• Faster matrix multiplication and inversion;
• Report on minor allele frequency, call frequencies (including partial calls) and missing allele rate
for SNPs;
Dairy Cattle Breeding and Genetics Committee Meeting, October 5, 2010. 1

• Report on homozygosity, call frequencies (including partial calls) and missing allele rate for
animals;
• If input genotypes are not sorted based on chromosome and position, gebv will now automatically
sort them and save them in a file (a utility program for this purpose is also included).
Modifications:
• Genotyping errors are no longer corrected (moved to the imputation program);
• Missing genotypes are no longer inferred (moved to the imputation program);
• The format of gebv_trait_name.txt output file was slightly modified;
• Very slight changes in the input parameter file.
Dairy Cattle Breeding and Genetics Committee Meeting, October 5, 2010. 2