Genomic structural diversity in Criollo Argentino horses: Analysis of copy number variations

Genomic Structural Diversity in Local Goats: Analysis of Copy-Number Variations

“…To further analyse the biological functions of the CNVRs, we conducted a GO analysis. Similar to the studies on CNVs carried out on other livestock species (e.g., [ 19 , 23 , 24 , 28 , 30 , 32 ]), the results showed that the functions of the proteins encoded by these genes included several biological processes, molecular functions, cellular components, and pathways, as reported in Table 2 . Among the most representative CNVRs, many of them included candidate genes associated with important breeding traits.…”

“…Moreover, all these factors could lead to a lack of overlap among the different studies on the same species. Nevertheless, our results could be considered reliable since the representation of the CNVRs in coat colour traits, immune related genes, and olfactory receptors was reported previously in livestock species [ 5 , 19 , 32 , 33 , 43 , 46 ]. Moreover, a biological link to traits, such as reproduction and behaviour, the immune response, and resistance/susceptibility to infectious diseases, which are known to be under selection, can be inferred for most genes within the CNVRs, and as reported above, the goat breeds involved in this study are well adapted to harsh environments and are resistant to infectious diseases.…”

“…The CNVR_33, CNVR_65, and CNVR_7 (frequency values of 0.411, 0.336, and 0.280, respectively) overlapped, with genes related to the immune system and belonging to several GO terms ( Table 2 ). In particular, CNVR_33 contain the T-cell receptors alpha chain V, which are important components in the adaptive immune system and that were described as the CNVs in Criollo Argentino horses [ 32 ] and in Brown Swiss dairy cattle [ 5 ]. The CNVR_65 contain the EXOC3L4 (exocyst complex component 3 like 4) and TNFAIP2 (TNF alpha induced protein 2) genes, which are associated with natural antibodies and considered as candidate genes for innate host defence and disease resistance in dairy cows [ 56 ].…”

“…Previous studies have completed genome-wide CNV analysis in many livestock species, including cattle [ 19 , 20 , 21 , 22 , 23 , 24 ], sheep [ 25 , 26 , 27 , 28 , 29 , 30 ], pigs [ 31 ], and horses [ 32 ]. However, in goats, only few studies have been conducted based on SNP array data (e.g., [ 13 , 33 ]).…”

Association analysis of SSTR2 copy number variation with cattle stature and its expression analysis in Chinese beef cattle

“…Numerous CNVs have been routinely identified using various genome analysis platforms, including single nucleotide polymorphism (SNP) genotyping platforms (Di Gerlando et al ., 2019), array comparative genomic hybridization (aCGH) (Zhang et al ., 2014) and next-generation sequencing (Xu et al ., 2017). These studies have been performed in humans (Altshuler et al ., 2010; Mills et al ., 2011), mice (Guryev et al ., 2008; Yalcin et al ., 2011), pigs (Wang et al ., 2013 a , 2014), horses (Doan et al ., 2013; Kader et al ., 2016; Corbi-Botto et al ., 2019), cattle (Jiang et al ., 2013; Yang et al ., 2017 a ), goats (Fontanesi et al ., 2010; Liu et al ., 2018; Zhang et al ., 2019) and chickens (Wang et al ., 2010). Over the past decades, significant progress has been made in mapping SNPs and insertions/deletions (Indels), the lengths of which are much smaller than those of CNVs, but there is less comprehensive annotation of CNVs (Pang et al ., 2010).…”