Copy number variation of individual cattle genomes using next-generation sequencing

Authors: Bickhart, Derek; HOU, YALI - University Of Maryland; Schroeder, Steven - Steve; ALKAN, CAN - University Of Washington Medical School; CARDONE, MARIA FRANCESCA - University Of Bari; MATUKUMALLI, LAKSHMI - Collaborator; SONG, JIUZHOU - University Of Maryland; SCHNABEL, ROBERT - University Of Missouri; VENTURA, MARIO - University Of Washington; TAYLOR, JEREMY - University Of Missouri; GARCIA, JOSE FERNANDO - Sao Paulo State University (UNESP); Van Tassell, Curtis - Curt; Sonstegard, Tad; EICHLER, EVAN - Howard Hughes Medical Institute; Liu, Ge - George

Submitted to: Genome Research
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 2/1/2012
Publication Date: 4/1/2012
Citation: Bickhart, D.M., Hou, Y., Schroeder, S.G., Alkan, C., Cardone, M., Matukumalli, L.K., Song, J., Schnabel, R.D., Ventura, M., Taylor, J., Garcia, J., Van Tassell, C.P., Sonstegard, T.S., Eichler, E.E., Liu, G. 2012. Copy number variation of individual cattle genomes using next-generation sequencing. Genome Research. 22(4):778-90.

Interpretive Summary: Copy Number Variations (CNVs), large insertions and deletions ranging from 1kb to 5Mb, affect a wide range of phenotypic traits; however, CNVs in or near complex duplicated regions are often difficult to track. Using a computational approach based on next generation sequencing (NGS), we examined genome-wide copy number differences among 6 cattle individuals from four breeds for beef, dairy or dual purpose. We identified thousands of CNV regions comprising ~56 Mbp sequence and over 1/3 of them are new discovery. We performed experimental confirmations and achieved a high validation rate. We detected and confirmed copy number differences for CATHL4, ULBP, KRTAP9-2, AFABP2, APOL3 and other genes. These candidate genes, which may have gone through breed-specific gene amplification and loss, could be responsible for specific traits in adaptation, health and production among cattle breeds. This is the first study of individualized cattle CNV maps and genome-wide gene copy number estimates. The ability to use NGS to accurately predict their copy number provides the first step to make genotype and phenotype correlations in these complex areas of the genome.

Technical Abstract: Copy Number Variations (CNVs) affect a wide range of phenotypic traits; however, CNVs in or near segmental duplication regions are often difficult to track. 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 been previously 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 like APOL3 and FABP2 were highly duplicated in beef breeds as compared to others. 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 SD maps and genome-wide gene copy number estimates, we enable future CNV studies into highly duplicated regions in the cattle genome.