Computational detection and experimental validation of segmental duplications and associated copy number variations in water buffalo (Bubalus bubalis)

Authors: LIU, SHULI - China Agricultural University; KANG, XIAOLONG - Ningxia University; CATACCHIO, CLAUDIA - University Of Bari; LIU, MEI - Northwest Agriculture And Forestry University; FANG, LINGZHAO - University Of Maryland; Schroeder, Steven - Steve; Li, Wenli; Rosen, Benjamin - Ben; IAMARTINO, DANIELA - Collaborator; IANNUZZI, LEOPOLDO - Collaborator; SONSTEGARD, TAD - Recombinetics, Inc; Van Tassell, Curtis - Curt; VENTURA, MARIO - University Of Bari; LOW, WAI YEE - University Of Adelaide; WILLIAMS, JOHN - University Of Adelaide; Bickhart, Derek; Liu, Ge - George

Submitted to: Functional and Integrative Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 1/9/2019
Publication Date: 5/1/2019
Citation: Liu, S., Kang, X., Catacchio, C.R., Liu, M., Fang, L., Schroeder, S.G., Li, W., Rosen, B.D., Iamartino, D., Iannuzzi, L., Sonstegard, T.S., Van Tassell, C.P., Ventura, M., Low, W., Williams, J.L., Bickhart, D.M., Liu, G. 2019. Computational detection and experimental validation of segmental duplications and associated copy number variations in water buffalo (Bubalus bubalis). Functional and Integrative Genomics. 19(3):409–419. https://doi.org/10.1007/s10142-019-00657-4.
DOI: https://doi.org/10.1007/s10142-019-00657-4

Interpretive Summary: Copy number variation (CNV) represents a major source of genomic variation. Using sequencing and other validation methods, we stuided CNV in water buffalo. These results fill our knowledge gaps and provide the foundation for future studies of CNV role in ruminants. Farmers, scientist, and policy planners who need improve animal health and production based on genome-enable animal selection will benefit from this study.

Technical Abstract: Duplicated sequences are an important source of gene innovation and structural variation within mammalian genomes. Using a read depth approach based on next-generation sequencing, we performed a genome-wide analysis of segmental duplications (SDs) and associated copy number variants (CNVs) in water buffalo (Bubalus bubalis). Aligning to the UMD3.1 cattle genome, we identified segmental duplications comprising 44.6 Mb (~1.73% of the cattle genome) of the autosomal and X chromosomal sequence in the genome of Olimpia (the water buffalo reference animal). We experimentally validated 70.3% (70/101) duplications using the fluorescent in situ hybridization. We also detected a total of 1344 CNV regions across 14 additional water buffalo individuals, amounting to 59.8Mb of variable sequence or 2.2% of the cattle genome. The CNV regions overlap 1245 genes and are significantly enriched for specific biological functions such as immune response, oxygen transport, sensory system and signalling transduction. Additionally, we performed array Comparative Genomic Hybridization (aCGH) experiments using the 14 water buffalos as test samples and Olimpia as the reference. Using a linear regression model, high Pearson correlations (r = 0.781) were observed between the digital aCGH values and aCGH probe log2 ratios. We further designed Quantitative PCR assays to confirm CNV regions within or near annotated genes and found 74.2% agreement with our CNV predictions. Our study confirms sub-chromosome-scale structural rearrangements present in the cattle-water buffalo lineage that may be useful in future selective breeding of both species.