Ility of Nguni cattle to handle harsh environmental conditions needs further
Ility of Nguni cattle to handle harsh environmental conditions needs further investigation. Nonsignificant overrepresentation by CNV genes in 3055 biological processes, 593 molecular functions and 391 cellular components was evident. These systems included cellular response to transforming growth factor beta stimulus, regulation of B cell proliferation and positive regulation of viral release from host cell functions. Previous findings have demonstrated CNVRs to be located in areas containing genes associated with environmental responses like sensory, defense and immunological functions and regulatory processors [31, 51]. Similar patterns are evident within Nguni cattle and suggest CNVs to potentially play an important role in the adaptative traits evident in Nguni cattle populations.CNVs and population structurebelong to sub-population A while 10 of the 11 animal genomes containing the CNVR on chromosome 4 (chr4:108834886?09130345) belonged to sub-population A. CNVR chr6:71910076?2118486 was present in 13 animals with 6 and 5 animals from sub-populations A and C respectively. Two hundred and eighty eight genes were identified to be associated with CNVRs in sub-populations A, B, C, D and E (Table 7). A number of genes only identified within specific sub-populations were present (Table 7). Sub-population A has the most (149) unique genes that are not recorded in the other sub-population groups. The ataxin 7-like 3B (ATXN7L3B) and tumor necrosis factor and alpha-induced protein 8 (TNFAIP8) genes were present in CNVRs in sub-populations B, C and E and A, C and E respectively and play a role in the immune system process, and the response to stress.CNVs and haplotype blocksCNV characteristics for each subpopulation are presented in Table 6. Sub-population A had the highest average number of CNVs per animal while sub-population D had the smallest average CNV length. Sub-population A had the ICG-001 web greatest number of animals in the study (n = 103) and also presented with the most CNVRs (n = 121) (Table 6). A number of CNVRs were shared between populations. The most widespread CNVR was identified on chromosome 6, covering the protocadherin 7 (PCDH7) and cysteine-rich hydrophobic domain 2 (CHIC2) genes and present in subpopulations A, B, C and E (Table 7). Increasing evidence has suggested that CNVs play a primary role in interindividual diversity [52], attributing to both normal phenotypic variation and major variations in complex traits such as susceptibility PubMed ID:https://www.ncbi.nlm.nih.gov/pubmed/26266977 to disease [53, 54]. Within Nguni cattle sub-populations a broad array of phenotypes are evident with great variations in coat colour, behaviour and immune response being evident [6]. As little research into the genotypic makeup of the Nguni PubMed ID:https://www.ncbi.nlm.nih.gov/pubmed/28607003 ecotypes has been performed, little is known about what differentiates these ecotypes on a genomic scale. Eighteen CNVRs were identified in multiple animals and are reported in Table 5. On closer inspection of these CNVRs, some noteworthy association can be seen. The CNVR located on chromosome 1 (chr1:104798012?105264358) was identified in 7 animals. Four of the animalsThirty four HPBs lay either within, across or adjacent to CNVRs identified within the Nguni cattle population (Additional file 7). Half of these occurances were at CNVR sites that were present in multiple individuals, with one such CNVR on chromosome 1 that was present in 17 animals (Additional file 7). Another HPB overlaped a CNVR associated with genes Ly1 antibody reactive homolog (LYAR), ne.