Copy Number Variants in Four Italian Turkey Breeds

Abstract

Heritage breeds can be considered a genetic reservoir of genetic variability to be conserved and valorized considering their historical, cultural, and adaptive characteristics and possibly for their high potential in commercial hybrid genetic improvement by gene introgression. The aim of the present research is to investigate via Copy Number Variant (CNVs) the genomic makeup of 4 Italian autochthonous turkey breeds (Bronzato Comune—BrCI, 24; Ermellinato di Rovigo—ErRo, 24; Parma e Piacenza—PrPc, 25; Romagnolo—RoMa, 29). CNVs detection was performed using two different software and an interbreed CNVs comparison was carried out. A total of 1077 CNVs were identified in 102 turkeys, summarized into 519 CNV regions (CNVRs), which resulted after merging in 101 and 18 breed and shared regions. Biodiversity was analyzed using the effective information supplied by CNVs analysis, and BrCI and ErRo were characterized by a low mapped CNV number. Differences were described at a genomic level related to physiological, reproductive, and behavioral traits. The comparison with other three Italian turkey breeds (Brianzolo, Colle Euganei, and Nero Italiano) using a CNV data set available in the literature showed high clustering properties at the genomic level, and their relationships are strictly linked to the geographical origin and to the history of the rural structure of their native regions.

Copy number variants in genomes of local sheep breeds from Russia

“…It has been shown that the CNVR makeup of livestock breeds depends on multiple factors such as past changes of effective population size, gene flow, breeding strategies, and selection (Upadhyay et al 2017;Strillacci et al 2021). The fact that more than a half of CNVRs detected in this study overlap CNVRs reported by others further confirms that our CNVR detection approaches worked and points to a shared genetic background of Russian and worldwide sheep breeds.…”

“…2017; Strillacci et al . 2021). The fact that more than a half of CNVRs detected in this study overlap CNVRs reported by others further confirms that our CNVR detection approaches worked and points to a shared genetic background of Russian and worldwide sheep breeds.…”

Genetic Diversity and Identification of Homozygosity-Rich Genomic Regions in Seven Italian Heritage Turkey (Meleagris gallopavo) Breeds

“…The intense selection for body weight in commercial turkeys determined a reduction in reproductive performance, as reported by Nestor et al, who discussed the genetics of growth and reproduction using the performance measured in over 40 generations of selection for 16-week body weight in turkey [ 37 ]. Interestingly, the PrPc, having the largest proportion of heterozygous individuals in this region (i.e., f(A) = f(B) = 0.50), is also the heaviest of all the Italian breeds [ 8 , 9 ] reaching an adult weight doubling the one of the other breeds (about 12 kg in males vs. 5–7 kg of other breeds; about 6.5 kg in females vs. 3–4 kg in other breeds). At present, the studies on genomic structure in turkeys are very limited as also recently pointed out by Adams et al [ 38 ] and, to best of our knowledge, no other published data are available on ROHs in hybrid turkeys or in selected pure lines.…”

“…In this study, 181 birds’ genotypes from the Axiom ® TurkeyHD Genotyping Array of seven Italian turkey breeds (Brianzolo: Brzl n. 31, Bronzato Comune: BrCI n. 24, Colle Euganei: CoEu n. 22, Parma e Piacenza: PrPc n. 25, Nero d’Italia: NeIt n. 26, Ermellinato di Rovigo: ErRo n. 24, and Romagnolo: Roma n. 29) were available from Strillacci et al (Brzl, NeIt, CoEu, and 12 samples of PrPc) and from Strillacci et al (BrCI, ErRo, Roma, and 13 samples of PrPc) [ 8 , 9 ]. The two genotype datasets were appended and underwent a joint quality control.…”

“…This occurred either where genomic selection (e.g., bovine breeds) has been adopted or in small and endangered populations where in situ genetic conservation plans are desired. Heritage turkey breeds were recently studied and, even if still limited, some indication about their genomic variability and diversity is nowadays available [ 4 , 5 , 6 , 7 , 8 , 9 ]. Recent studies were performed on run of homozygosity (ROH): Marras et al characterized ROH-rich regions in a commercial turkey hybrid, and Strillacci et al discussed the difference in ROH between the autochthonous Mexican and commercial hybrid turkeys [ 10 , 11 ].…”