I think the easiest option is to grep each breed and output the count:

grep 'SIM001' mymultisample.vcf | wc

If you have a list of breeds in your multisample vcf, create a for loop:

for breed in $(<listofbreeds.txt); do grep '$breed' mymultisample.vcf |wc ; done

So if I understand correctly, you have a VCF file with about 1000 samples that represent 7 different breeds of animal. Each sample is named in a consistent fashion, with a prefix (e.g. "FLV" or "SIM") and then a number.

You could use GATKs SelectVariant tool to subset your VCF into 7 files, one for each breed, by using either the -select_expressions or the -sample_file parameters. I'm not super awesome with regex, but perhaps the following would work:

java -jar GenomeAnalysisTK.jar -R <reference.fa> -T SelectVariants -V <vcf_file> -se 'SIM.+' -o sim.vcf

Alternatively, it may just be easier to use the sample_file flag - make a file for each breed that has a list of the sample names, and then pass that to GATK:

 java -jar GenomeAnalysisTK.jar -R <reference.fa> -T SelectVariants -V <vcf_file> -sf <list_of_all_SIM_samples.txt> -o sim.vcf

And then just repeat for each breed.