ARS | Publication request: Individualized cattle copy number and segmental duplication maps using next generation sequencing

Submitted to: Meeting Abstract
Publication Type: Abstract Only
Publication Acceptance Date: September 22, 2011
Publication Date: October 20, 2011
Citation: Bickhart, D.M., Hou, Y., Schroeder, S.G., Alkan, C., Cardone, M., Matukumalli, L., Song, J., Schnabel, R.D., Ventura, M., Taylor, J.F., Garcia, J., Eichler, E.E., Sonstegard, T.S., Van Tassell, C.P., Liu, G. 2011. Individualized cattle copy number and segmental duplication maps using next generation sequencing. Meeting Abstract. No. 8.

Technical Abstract: Copy Number Variations (CNVs) affect a wide range of phenotypic traits; however, CNVs in or near segmental duplication regions are often intractable. Using a read depth approach based on next generation sequencing, we examined genome-wide copy number differences among five taurine (three Angus, one Holstein and one Hereford) and one indicine (Nelore) cattle. In placed chromosomes, we identified 1265 CNV regions comprising ~55.6 Mbp sequence and 476 of which (~38%) have not previously been reported. We validated this sequence-based CNV call set with aCGH, qPCR and FISH, achieving an 82% validation rate with an 8% false positive rate. We further estimated absolute copy numbers for genomic segments and annotated genes in each individual. Surveys of the top 25 most variable genes revealed that the Nelore individual had the lowest copy numbers in 13 cases (~52%, chi squared test, p value < 0.05). In contrast, genes related to pathogen and parasite-resistance such as CATHL4 and ULBP17 were highly duplicated in the Nelore individual relative to the taurine cattle, while genes involved in lipid transport and metabolism including APOL3 and FABP2 were highly duplicated in the beef breeds. These CNV regions also harbor genes like BSP30A and WC1, suggesting that some CNVs may be associated with breed-specific differences in adaptation, health and production traits. By providing the first individualized cattle CNV and segmental duplication maps and genome-wide gene copy number estimates, we enable future CNV studies into highly duplicated regions in the cattle genome.