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For: Moradi MH, Khaltabadi-farahani AH, Khodaei-motlagh M, Kazemi-bonchenari M, Mcewan J. Genome-wide selection of discriminant SNP markers for breed assignment in indigenous sheep breeds. Annals of Animal Science 2021;21:807-31. [DOI: 10.2478/aoas-2020-0097] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]

For:	Moradi MH, Khaltabadi-farahani AH, Khodaei-motlagh M, Kazemi-bonchenari M, Mcewan J. Genome-wide selection of discriminant SNP markers for breed assignment in indigenous sheep breeds. Annals of Animal Science 2021;21:807-31. [DOI: 10.2478/aoas-2020-0097] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]

Number

Cited by Other Article(s)

Bayraktar M. Analysing the genetic diversity of three sheep breeds in Turkey and nearby countries using 50 K SNPs data. Anim Biotechnol 2024;35:2329106. [PMID: 38497403 DOI: 10.1080/10495398.2024.2329106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]

Moradi MH, Mahmodi R, Farahani AHK, Karimi MO. Genome-wide evaluation of copy gain and loss variations in three Afghan sheep breeds. Sci Rep 2022;12:14286. [PMID: 35996004 PMCID: PMC9395407 DOI: 10.1038/s41598-022-18571-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 08/16/2022] [Indexed: 11/23/2022] Open

Abstract

Copy number variation (CNV) is one of the main sources of variation between different individuals that has recently attracted much researcher interest as a major source for heritable variation in complex traits. The aim of this study was to identify CNVs in Afghan indigenous sheep consisting of three Arab, Baluchi, and Gadik breeds using genomic arrays containing 53,862 single nucleotide polymorphism (SNP) markers. Data were analyzed using the Hidden Markov Model (HMM) of PennCNV software. In this study, out of 45 sheep studied, 97.8% (44 animals) have shown CNVs. In total, 411 CNVs were observed for autosomal chromosomes and the entire sequence length of around 144 Mb was identified across the genome. The average number of CNVs per each sheep was 9.13. The identified CNVs for Arab, Baluchi, and Gadik breeds were 306, 62, and 43, respectively. After merging overlapped regions, a total of 376 copy number variation regions (CNVR) were identified, which are 286, 50, and 40 for Arab, Baluchi, and Gadik breeds, respectively. Bioinformatics analysis was performed to identify the genes and QTLs reported in these regions and the biochemical pathways involved by these genes. The results showed that many of these CNVRs overlapped with the genes or QTLs that are associated with various pathways such as immune system development, growth, reproduction, and environmental adaptions. Furthermore, to determine a genome-wide pattern of selection signatures in Afghan sheep breeds, the unbiased estimates of FST was calculated and the results indicated that 37 of the 376 CNVRs (~ 10%) have been also under selection signature, most of those overlapped with the genes influencing production, reproduction and immune system. Finally, the statistical methods used in this study was applied in an external dataset including 96 individuals of the Iranian sheep breed. The results indicated that 20 of the 114 CNVRs (18%) identified in Iranian sheep breed were also identified in our study, most of those overlapped with the genes influencing production, reproduction and immune system. Overall, this is the first attempts to develop the genomic map of loss and gain variation in the genome of Afghan indigenous sheep breeds, and may be important to shed some light on the genomic regions associated with some economically important traits in these breeds.

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Lei Z, Sun W, Guo T, Li J, Zhu S, Lu Z, Qiao G, Han M, Zhao H, Yang B, Zhang L, Liu J, Yuan C, Yue Y. Genome-Wide Selective Signatures Reveal Candidate Genes Associated with Hair Follicle Development and Wool Shedding in Sheep. Genes (Basel) 2021;12:genes12121924. [PMID: 34946875 PMCID: PMC8702090 DOI: 10.3390/genes12121924] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 11/25/2021] [Accepted: 11/27/2021] [Indexed: 02/03/2023] Open

Affiliation(s)

Zhihui Lei Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; (Z.L.); (W.S.); (T.G.); (J.L.); (Z.L.); (G.Q.); (M.H.); (H.Z.); (B.Y.); (J.L.); (C.Y.) College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China; (S.Z.); (L.Z.)
Weibo Sun Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; (Z.L.); (W.S.); (T.G.); (J.L.); (Z.L.); (G.Q.); (M.H.); (H.Z.); (B.Y.); (J.L.); (C.Y.)
Tingting Guo Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; (Z.L.); (W.S.); (T.G.); (J.L.); (Z.L.); (G.Q.); (M.H.); (H.Z.); (B.Y.); (J.L.); (C.Y.)
Jianye Li Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; (Z.L.); (W.S.); (T.G.); (J.L.); (Z.L.); (G.Q.); (M.H.); (H.Z.); (B.Y.); (J.L.); (C.Y.)
Shaohua Zhu College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China; (S.Z.); (L.Z.)
Zengkui Lu Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; (Z.L.); (W.S.); (T.G.); (J.L.); (Z.L.); (G.Q.); (M.H.); (H.Z.); (B.Y.); (J.L.); (C.Y.)
Guoyan Qiao Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; (Z.L.); (W.S.); (T.G.); (J.L.); (Z.L.); (G.Q.); (M.H.); (H.Z.); (B.Y.); (J.L.); (C.Y.)
Mei Han Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; (Z.L.); (W.S.); (T.G.); (J.L.); (Z.L.); (G.Q.); (M.H.); (H.Z.); (B.Y.); (J.L.); (C.Y.)
Hongchang Zhao Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; (Z.L.); (W.S.); (T.G.); (J.L.); (Z.L.); (G.Q.); (M.H.); (H.Z.); (B.Y.); (J.L.); (C.Y.)
Bohui Yang Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; (Z.L.); (W.S.); (T.G.); (J.L.); (Z.L.); (G.Q.); (M.H.); (H.Z.); (B.Y.); (J.L.); (C.Y.)
Liping Zhang College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China; (S.Z.); (L.Z.)
Jianbin Liu Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; (Z.L.); (W.S.); (T.G.); (J.L.); (Z.L.); (G.Q.); (M.H.); (H.Z.); (B.Y.); (J.L.); (C.Y.)
Chao Yuan Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; (Z.L.); (W.S.); (T.G.); (J.L.); (Z.L.); (G.Q.); (M.H.); (H.Z.); (B.Y.); (J.L.); (C.Y.)
Yaojing Yue Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; (Z.L.); (W.S.); (T.G.); (J.L.); (Z.L.); (G.Q.); (M.H.); (H.Z.); (B.Y.); (J.L.); (C.Y.) Correspondence:

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