Selecting Homozygous Goat Reference Genome

A DNA panel composed of 96 U.S. goats from 6 breeds (35 Boer, 11 Kiko, 12 LaMancha, 15 Myotonic, 3 San Clemente, and 20 Spanish) was assembled to identify the most homozygous individual so as to minimize the number of scaffold conflicts due to heterozygous genomic regions^{57 (link)}. Genotypes were generated using Illumina’s Caprine53K SNP beadchip processed through Genome Studio (Illumina, Inc. San Diego, CA). The degrees of homozygosity of individuals were determined by raw counts of homozygous markers on the genotyping chip (Sayre, B.L., Sonstegard, T.S., Silverstein, J., Huson, H.J., Woodward-Greene, J., et al. Proceedings of the Brazilian Society of Animal Science, Campinas, SP, BR (2013)). Individuals were ranked by their counts of homozygous markers and the individual with the highest count was selected as the reference animal. An adult male of the San Clemente goat breed with 46.02% SNP-distance homozygosity (FROH) was selected from this survey as the reference animal.

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Bickhart D.M., Rosen B.D., Koren S., Sayre B.L., Hastie A.R., Chan S., Lee J., Lam E.T., Liachko I., Sullivan S.T., Burton J.N., Huson H.J., Nystrom J.C., Kelley C.M., Hutchison J.L., Zhou Y., Sun J., Crisà A., de León F.A., Schwartz J.C., Hammond J.A., Waldbieser G.C., Schroeder S.G., Liu G.E., Dunham M.J., Shendure J., Sonstegard T.S., Phillippy A.M., Van Tassell C.P, & Smith T.P. (2017). Single-molecule sequencing and chromatin conformation capture enable de novo reference assembly of the domestic goat genome. Nature genetics, 49(4), 643-650.

Publication 2017

Genome Studio

A dna Adult Animal Chip Genome Goat Heterozygous Homozygosity Male Spanish

Corresponding Organization :

Other organizations : Agricultural Research Service, National Human Genome Research Institute, Virginia State University, BioNano Genomics (United States), University of Washington, ID Genomics (United States), Cornell University, Roman L. Hruska U.S. Meat Animal Research Center, Northwest A&F University, South China Agricultural University, Consiglio per la ricerca in agricoltura e l’analisi dell’economia agraria, University of Minnesota, The Pirbright Institute, Howard Hughes Medical Institute, Recombinetics (United States)

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Variable analysis

independent variables

Breed of goats (Boer, Kiko, LaMancha, Myotonic, San Clemente, Spanish)

dependent variables

Degree of homozygosity (raw counts of homozygous markers)

control variables

Genotyping platform (Illumina's Caprine53K SNP beadchip)
Genotype analysis software (Genome Studio)

controls

The individual with the highest count of homozygous markers was selected as the reference animal.

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