Detection of copy number variants in African goats using whole genome sequence data

Authors: NANDOLO, WILSON - University Of Natural Resources & Applied Life Sciences - Austria; MESZAROS, GABOR - University Of Natural Resources & Applied Life Sciences - Austria; BANDA, LIVENESS - Lilongwe University Of Agriculture And Natural Resources; GONDWE, TIMOTHY - Lilongwe University Of Agriculture And Natural Resources; MULINDWA, HENRY - National Livestock Research Institute; NAKIMBUGWE, HELEN - Collaborator; WURZINGER, MARIA - University Of Natural Resources & Applied Life Sciences - Austria; CLARK, EMILY - University Of Edinburgh; Woodward-Greene, Jennifer; LIU, MEI - Northwest Agriculture And Forestry University; Liu, Ge - George; Van Tassell, Curtis - Curt; Rosen, Benjamin - Ben; SOLKNER, JOHANN - University Of Natural Resources & Applied Life Sciences - Austria

Submitted to: BMC Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 5/11/2021
Publication Date: 5/29/2021
Citation: Nandolo, W., Meszaros, G., Banda, L.J., Gondwe, T.N., Mulindwa, H.A., Nakimbugwe, H.N., Wurzinger, M., Clark, E., Woodward Greene, M.J., Liu, M., Liu, G., Van Tassell, C.P., Rosen, B.D., Solkner, J. 2021. Detection of copy number variants in African goats using whole genome sequence data. BMC Genomics. 22(1):398. https://doi.org/10.1186/s12864-021-07703-1.
DOI: https://doi.org/10.1186/s12864-021-07703-1

Interpretive Summary: Copy number variations (CNV) are a phenomenon where sections of a genome are repeated and the number of repeats differ between individuals of a species. Structural variation (SV) is the relatively large differences between individuals in the structure of their genomes. In this study CNV were defined as SV duplications or deletions longer than 50 base pairs (bp). The CNV represent a significant source of variation in the genome. As a result, understanding CNV are essential to the genetic characterization of animal breeds. The aim of this study was to develop a detailed CNV map for African goats. Sequence data of 182 goats was generated representing 34 breeds from 9 Sub-Saharan African countries: Ethiopia, Kenya, Madagascar, Malawi, Mali, Mozambique, Tanzania, Uganda, and Zimbabwe. These countries were assigned to 5 populations according to geographical location. These populations were used to detect SV. CNV regions (CNVR) were identified by merging overlapping CNV. Identification of functional elements was performed for genes that were in CNV and showed high differentiation between and within populations. A total of 253,553 CNV were identified, 244,876 deletions and 8,677 duplications. Results identified an overall average of 1,393 CNV per animal. The mean CNV length was 3.3 kilo-bases (kb - 1000 bp), with a median of 1.3 kb. Overall, the West African (WAF) population had longer CNV (mean 4.0 kb) than the other sub-groups. There was substantial differences between the populations for some CNV, suggestive of the effect of population-specific selective pressures. A total of 6,231 global CNVR were found across all animals, representing 59.2 Mb (2.4%) of the goat genome. About 1.6% of the CNVR were present in all 34 breeds and 28.7% were present in all the 5 populations. The CNVR had genes that were highly enriched in important biological functions, molecular functions, and cellular components. The study presents the first fine CNV map of African goat based on WGS data and adds to the growing body of knowledge on the genetic characterization of goats.

Technical Abstract: Copy number variations (CNV) are a significant source of variation in the genome, as such they are essential to the genetic characterization of animal breeds. The aim of this study was to develop a fine-scaled CNV map for African goats. Sequence data of 182 goats representing 34 breeds from 9 Sub-Saharan African countries (Ethiopia, Kenya, Madagascar, Malawi, Mali, Mozambique, Tanzania, Uganda, and Zimbabwe), divided into 5 populations according to geographical location, were used to detect structural variation (SV). CNV were defined as SV duplications or deletions longer than 50 bp. CNV regions (CNVR) were computed by merging overlapping CNV. Functional annotation was performed for genes that were in CNV that showed high differentiation between and within populations. A total of 253,553 CNV (244,876 deletions and 8,677 duplications) were identified, corresponding to an overall average of 1,393 CNV per animal. The mean CNV length was 3.3 kb, with a median of 1.3 kb. Overall, the West African (WAF) population had longer CNV (mean 4.0 kb) than the other sub-groups. There was substantial differentiation between the populations for some CNV, suggestive of the effect of population-specific selective pressures. A total of 6,231 global CNVR were found across all animals, representing 59.2 Mb (2.4%) of the goat genome. About 1.6% of the CNVR were present in all 34 breeds and 28.7% were present in all the 5 populations. The CNVR had genes that were highly enriched in important biological functions, molecular functions, and cellular components including retrograde endocannabinoid signaling, glutamatergic synapse and circadian entrainment. The study presents the first fine CNV map of African goat based on WGS data and adds to the growing body of knowledge on the genetic characterization of goats.