Identification and population genetic analyses of copy number variations in six domestic goat breeds and Bezoar ibexes using next-generation sequencing

- analyses of copy number variations in six domestic goat breeds and Bezoar ibexes using next-generation sequencing.
- Keywords: Goat, Copy number variations, Short-read sequencing, Comparative genomics.
- Full list of author information is available at the end of the article.
- A well-known example of positive selection is that the copy number of the salivary amylase (AMY1) gene highly differs be- tween the human populations with high-starch diets and those with traditionally low-starch diets [9].
- Based on the ADAPTmap data, Liu et al.
- CNVs distribute ubiquitously in the goat genome.
- (ARS1), the second runs of whole-genome sequencing data of the nine goats showed coverage depth of 25×.
- These CNVRs covered 266.71 Mb (10.80%) of the goat.
- 1 Genome-wide characteristics of CNVs in the goat genome.
- a A distribution histogram of the CNV length.
- The total number and length of the CNVRs identified in each population were provided in Add- itional file 5..
- To further examine the credibility of the CNVRs de- tected in this study, we compared the CNV genes with those in the Goat Pan-genome database (hereafter re- ferred to as Pangoat for simplicity) and a previous study [7] that used SNP data from the ADAPTmap project (see details in Methods).
- 2 Summary of the copy number variable genes identified in the seven goat populations.
- a Comparison of the identified copy number variable genes with two other large-scale datasets.
- Based on the 5% right tail (i.e., F ST ≥ 0.318) of the empirical F ST.
- 3 Population genetics analyses of the seven goat populations based on genome-wide deletion and duplication genotypes.
- Based on the 5% right tail (i.e., F ST ≥ 0.282) of the empirical F ST.
- The characteristics of CNVs in the goat genome.
- However, there were fewer shared CNV genes (e.g., ADAMTS20, ASIP, and DGAT1) between our work and the result obtained from the ADAPTmap data [7], which can be explained by differ- ent sampled populations (i.e., the ADAPTmap data.
- In contrast, the whole-genome sequencing data of the goat samples from three other domestic goat breeds (i.e., SC, MD, and MN) and Bezoar ibexes were downloaded from NCBI.
- 25×) for nine sampled goats (i.e., three individuals in each of the CB, JT, and TC goat breeds).
- List of the primer information for the validation of CNVs by PCR and qPCR..
- CNV: Copy number variation;.
- Mills RE, Walter K, Stewart C, Handsaker RE, Chen K, Alkan C, et al.
- Mapping copy number variation by population-scale genome sequencing.
- Wright D, Boije H, Meadows JRS, Bed'hom B, Gourichon D, Vieaud A, et al..
- Copy number variation in intron 1 of SOX5 causes the pea-comb phenotype in chickens.
- Dorshorst B, Molin A-M, Rubin C-J, Johansson AM, Strömstedt L, Pham M-H, et al.
- Menzi F, Keller I, Reber I, Beck J, Brenig B, Schütz E, et al.
- Carneiro M, Hu D, Archer J, Feng C, Afonso S, Chen C, et al.
- Kadri NK, Sahana G, Charlier C, Iso-Touru T, Guldbrandtsen B, Karim L, et al..
- Liu M, Zhou Y, Rosen BD, Van Tassell CP, Stella A, Tosser-Klopp G, et al..
- Diversity of copy number variation in the worldwide goat population..
- Fontanesi L, Martelli PL, Beretti F, Riggio V, Dall'Olio S, Colombo M, et al.
- An initial comparative map of copy number variations in the goat (Capra hircus) genome.
- Perry GH, Dominy NJ, Claw KG, Lee AS, Fiegler H, Redon R, et al.
- Diet and the evolution of human amylase gene copy number variation.
- Xue Y, Sun D, Daly A, Yang F, Zhou X, Zhao M, et al.
- Adaptive evolution of UGT2B17 copy-number variation.
- Hasin Y, Olender T, Khen M, Gonzaga-Jauregui C, Kim PM, Urban AE, et al..
- High-resolution copy-number variation map reflects human olfactory receptor diversity and evolution.
- Exploring the role of copy number variants in human adaptation.
- Axelsson E, Ratnakumar A, Arendt M-L, Maqbool K, Webster MT, Perloski M, et al.
- Xu L, Hou Y, Bickhart DM, Zhou Y, EHa H, Song J, et al.
- Population-genetic properties of differentiated copy number variations in cattle.
- Dong Y, Zhang X, Xie M, Arefnezhad B, Wang Z, Wang W, et al.
- Cai Y, Fu W, Cai D, Heller R, Zheng Z, Wen J, et al.
- Evolutionary changes of the number of olfactory receptor genes in the human and mouse lineages.
- Letaief R, Rebours E, Grohs C, Meersseman C, Fritz S, Trouilh L, et al..
- Identification of copy number variation in French dairy and beef breeds using next-generation sequencing.
- Yang L, Xu L, Zhou Y, Liu M, Wang L, Kijas JW, et al.
- Diversity of copy number variation in a worldwide population of sheep.
- Jiang J, Wang J, Wang H, Zhang Y, Kang H, Feng X, et al.
- Global copy number analyses by next generation sequencing provide insight into pig genome variation.
- Sudmant PH, Mallick S, Nelson BJ, Hormozdiari F, Krumm N, Huddleston J, et al.
- Global diversity, population stratification, and selection of human copy-number variation.
- Mechanisms of change in gene copy number.
- Mutations in the agouti (ASIP), the extension (MC1R), and the brown (TYRP1) loci and their association to coat color phenotypes in horses (Equus caballus).
- Drögemüller C, Giese A, Martins-Wess F, Wiedemann S, Andersson L, Brenig B, et al.
- Fontanesi L, Beretti F, Riggio V, Gómez González E, Dall ’ Olio S, Davoli R, et al.
- Copy number variation and missense mutations of the Agouti.
- Grisart B, Coppieters W, Farnir F, Karim L, Ford C, Berzi P, et al.
- regulation of the physiology of pregnancy.
- Copy-number variation in goat genome sequence: a comparative analysis of the different litter size trait groups.
- Guo J, Zhong J, Li L, Zhong T, Wang L, Song T, et al.
- Diversity and regulatory impact of copy number variation in the primate Macaca fascicularis.
- Bickhart DM, Hou Y, Schroeder SG, Alkan C, Cardone MF, Matukumalli LK, et al.
- Copy number variation of individual cattle genomes using next- generation sequencing.
- Cozzi MC, Martinez-Ruiz CP, Roman-Ponce SI, Murillo VEV, Utrera ÁR, Montaño-Bermúdez MM, et al.
- Copy number variants reveal genomic diversity in a Mexican creole cattle population.
- Peng S-J, Cao X-K, Dong D, Liu M, Hao D, Shen X-M, et al.
- Paudel Y, Madsen O, Megens H-J, Frantz LAF, Bosse M, Bastiaansen JWM, et al.
- Evolutionary dynamics of copy number variation in pig genomes in the context of adaptation and domestication.
- Santi CM, Martínez-López P, de la Vega-Beltrán JL, Butler A, Alisio A, Darszon A, et al.
- Stafuzza NB, RMdO S, BdO F, Masuda Y, Huang Y, Gray K, et al.
- A genome- wide single nucleotide polymorphism and copy number variation analysis for number of piglets born alive.
- Xing J, Wuren T, Simonson TS, Watkins WS, Witherspoon DJ, Wu W, et al..
- Lou H, Lu Y, Lu D, Fu R, Wang X, Feng Q, et al.
- Zhang X, Wang K, Wang L, Yang Y, Ni Z, Xie X, et al.
- Genome-wide patterns of copy number variation in the Chinese yak genome.
- Multi-ethnic cytochrome-P450 copy number profiling: novel pharmacogenetic alleles and mechanism of copy number variation formation.
- Gene copy number variations: it is important to determine which allele is affected.
- Differential quantification of CYP2D6 gene copy number by four different.
- Consequences of CYP2D6 copy-number variation for pharmacogenomics in psychiatry.
- A genome wide study of genetic adaptation to high altitude in feral Andean horses of the páramo.
- Hou C-L, Meng F-H, Wang W, Wang S-Y, Xing Y-P, Cao J-W, et al.
- Genome- wide analysis of copy number variations in Chinese sheep using array comparative genomic hybridization.
- Wang X, Liu J, Zhou G, Guo J, Yan H, Niu Y, et al.
- Li X, Su R, Wan W, Zhang W, Jiang H, Qiao X, et al.
- Wang X, Yu H, Lei A, Zhou J, Zeng W, Zhu H, et al.
- Wang X, Cai B, Zhou J, Zhu H, Niu Y, Ma B, et al.
- Li W-R, Liu C-X, Zhang X-M, Chen L, Peng X-R, He S-G, et al.
- Li Y, Song S, Liu X, Zhang Y, Wang D, He X, et al.
- McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, Kernytsky A, et al..
- Wang X, Zheng Z, Cai Y, Chen T, Li C, Fu W, et al.
- Redon R, Ishikawa S, Fitch KR, Feuk L, Perry GH, Andrews TD, et al.
- Global variation in copy number in the human genome.
- Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, et al.
- Danecek P, Auton A, Abecasis G, Albers CA, Banks E, DePristo MA, et al.
- Raudvere U, Kolberg L, Kuzmin I, Arak T, Adler P, Peterson H, et al

Xem thử không khả dụng, vui lòng xem tại trang nguồn
hoặc xem Tóm tắt