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Zhang K, Mi F, Li X, Wang Z, Jiang F, Song E, Guo P, Lan X. Detection of genetic variation in bovine CRY1 gene and its associations with carcass traits. Anim Biotechnol 2023; 34:3387-3394. [PMID: 36448652 DOI: 10.1080/10495398.2022.2149547] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
The biological clock (also known as circadian clock) is closely related to growth and development, metabolism, and diseases in animals. As a part of the circadian clock, the cryptochrome circadian regulator 1 (CRY1) gene is involved in the regulation of biological processes such as osteogenesis, energy metabolism and cell proliferation, however, few studies have been reported on the relationship between this gene and animal carcass traits. Herein, a total of four insertion/deletion (InDel) loci within the CRY1 gene were detected in Shandong Black Cattle Genetic Resource (SDBCGR) population (n = 433). Among them, the P1-6-bp-del locus was polymorphic in population of interest. Moreover, the P1-6-bp-del locus showed two genotypes, with a higher insertion/insertion (II) genotype frequency (0.751) than insertion/deletion (ID) genotype frequency (0.249). Correlation analysis showed that the P1-6-bp-del locus polymorphisms were significantly associated with twenty carcass traits (e.g., slaughter weight, limb weight, and belly meat weight). Individuals with II genotype were significantly better than those with ID genotype for eighteen carcass traits. Therefore, the P1-6-bp-del locus of the CRY1 gene can be used as a molecular marker for beef cattle breeding.
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Affiliation(s)
- Kejing Zhang
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Fang Mi
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
- National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Xuelan Li
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Zhiying Wang
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Fugui Jiang
- Shandong Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Enliang Song
- Shandong Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Peng Guo
- College of Computer and Information Engineering, Tianjin Agricultural University, Tianjin, China
| | - Xianyong Lan
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
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Amandykova M, Akhatayeva Z, Kozhakhmet A, Kapassuly T, Orazymbetova Z, Yergali K, Khamzin K, Iskakov K, Dossybayev K. Distribution of Runs of Homozygosity and Their Relationship with Candidate Genes for Productivity in Kazakh Meat-Wool Sheep Breed. Genes (Basel) 2023; 14:1988. [PMID: 38002931 PMCID: PMC10671688 DOI: 10.3390/genes14111988] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2023] [Revised: 10/17/2023] [Accepted: 10/23/2023] [Indexed: 11/26/2023] Open
Abstract
Increasing the fertility of sheep remains one of the crucial issues of modern sheep breeding. The Kazakh meat-wool sheep is an excellent breed with high meat and wool productivity and well adapted to harsh conditions. Nowadays, runs of homozygosity (ROHs) are considered a suitable approach for studying the genetic characteristics of farm animals. The aims of the study were to analyze the distribution of ROHs, describe autozygosity, and detect genomic regions with high ROH islands. In this study, we genotyped a total of 281 Kazakh meat-wool sheep using the Illumina iScan® system (EquipNet, Canton, MA, USA) via Ovine SNP50 BeadChip array. As a results, a total of 15,069 ROHs were found in the three Kazakh meat-wool sheep populations. The mean number of ROH per animal across populations varied from 40.3 (POP1) to 42.2 (POP2) in the category 1+ Mb. Furthermore, the number of ROH per animal in ROH1-2 Mb were much higher than ROH2-4 Mb and ROH8-16 Mb in the three sheep populations. Most of individuals had small number of ROH>16 Mb. The highest and lowest genomic inbreeding coefficient values were observed in POP2 and POP3, respectively. The estimated FROH presented the impact that recent inbreeding has had in all sheep populations. Furthermore, a set of interesting candidate genes (BMP2, BMPR2, BMPRIB, CLOCK, KDM2B, TIAM1, TASP1, MYBPC1, MYOM1, and CACNA2D1), which are related to the productive traits, were found. Collectively, these findings will contribute to the breeding and conservation strategies of the Kazakh meat-wool sheep breed.
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Affiliation(s)
- Makpal Amandykova
- Laboratory of Animal Genetics and Cytogenetics, Institute of Genetics and Physiology SC MSHE RK, Al-Farabi Ave. 93, Almaty 050060, Kazakhstan; (M.A.); (Z.A.); (A.K.); (T.K.); (Z.O.); (K.Y.); (K.I.)
- Department of Molecular Biology and Genetics, Faculty of Biology and Biotechnology, Al-Farabi Kazakh National University, Al-Farabi Ave. 71, Almaty 050042, Kazakhstan
| | - Zhanerke Akhatayeva
- Laboratory of Animal Genetics and Cytogenetics, Institute of Genetics and Physiology SC MSHE RK, Al-Farabi Ave. 93, Almaty 050060, Kazakhstan; (M.A.); (Z.A.); (A.K.); (T.K.); (Z.O.); (K.Y.); (K.I.)
- Laboratory of Molecular Genetics, Kazakh Research Institute of Livestock and Fodder Production, Zhandosov Str. 51, Almaty 050035, Kazakhstan;
| | - Altynay Kozhakhmet
- Laboratory of Animal Genetics and Cytogenetics, Institute of Genetics and Physiology SC MSHE RK, Al-Farabi Ave. 93, Almaty 050060, Kazakhstan; (M.A.); (Z.A.); (A.K.); (T.K.); (Z.O.); (K.Y.); (K.I.)
- Department of Molecular Biology and Genetics, Faculty of Biology and Biotechnology, Al-Farabi Kazakh National University, Al-Farabi Ave. 71, Almaty 050042, Kazakhstan
- Laboratory of Molecular Genetics, Kazakh Research Institute of Livestock and Fodder Production, Zhandosov Str. 51, Almaty 050035, Kazakhstan;
| | - Tilek Kapassuly
- Laboratory of Animal Genetics and Cytogenetics, Institute of Genetics and Physiology SC MSHE RK, Al-Farabi Ave. 93, Almaty 050060, Kazakhstan; (M.A.); (Z.A.); (A.K.); (T.K.); (Z.O.); (K.Y.); (K.I.)
- Department of Molecular Biology and Genetics, Faculty of Biology and Biotechnology, Al-Farabi Kazakh National University, Al-Farabi Ave. 71, Almaty 050042, Kazakhstan
| | - Zarina Orazymbetova
- Laboratory of Animal Genetics and Cytogenetics, Institute of Genetics and Physiology SC MSHE RK, Al-Farabi Ave. 93, Almaty 050060, Kazakhstan; (M.A.); (Z.A.); (A.K.); (T.K.); (Z.O.); (K.Y.); (K.I.)
| | - Kanagat Yergali
- Laboratory of Animal Genetics and Cytogenetics, Institute of Genetics and Physiology SC MSHE RK, Al-Farabi Ave. 93, Almaty 050060, Kazakhstan; (M.A.); (Z.A.); (A.K.); (T.K.); (Z.O.); (K.Y.); (K.I.)
- Laboratory of Molecular Genetics, Kazakh Research Institute of Livestock and Fodder Production, Zhandosov Str. 51, Almaty 050035, Kazakhstan;
| | - Kadyrzhan Khamzin
- Laboratory of Molecular Genetics, Kazakh Research Institute of Livestock and Fodder Production, Zhandosov Str. 51, Almaty 050035, Kazakhstan;
| | - Kairat Iskakov
- Laboratory of Animal Genetics and Cytogenetics, Institute of Genetics and Physiology SC MSHE RK, Al-Farabi Ave. 93, Almaty 050060, Kazakhstan; (M.A.); (Z.A.); (A.K.); (T.K.); (Z.O.); (K.Y.); (K.I.)
- Laboratory of Molecular Genetics, Kazakh Research Institute of Livestock and Fodder Production, Zhandosov Str. 51, Almaty 050035, Kazakhstan;
| | - Kairat Dossybayev
- Laboratory of Animal Genetics and Cytogenetics, Institute of Genetics and Physiology SC MSHE RK, Al-Farabi Ave. 93, Almaty 050060, Kazakhstan; (M.A.); (Z.A.); (A.K.); (T.K.); (Z.O.); (K.Y.); (K.I.)
- Department of Molecular Biology and Genetics, Faculty of Biology and Biotechnology, Al-Farabi Kazakh National University, Al-Farabi Ave. 71, Almaty 050042, Kazakhstan
- Laboratory of Molecular Genetics, Kazakh Research Institute of Livestock and Fodder Production, Zhandosov Str. 51, Almaty 050035, Kazakhstan;
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Chang C, He X, Di R, Wang X, Han M, Liang C, Chu M. Thyroid Transcriptomic Profiling Reveals the Follicular Phase Differential Regulation of lncRNA and mRNA Related to Prolificacy in Small Tail Han Sheep with Two FecB Genotypes. Genes (Basel) 2022; 13:genes13050849. [PMID: 35627234 PMCID: PMC9141851 DOI: 10.3390/genes13050849] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2022] [Revised: 05/05/2022] [Accepted: 05/07/2022] [Indexed: 11/16/2022] Open
Abstract
Long non-coding RNA (lncRNA) accounts for a large proportion of RNA in animals. The thyroid gland has been established as an important gland involved in animal reproduction, however, little is known of its gene expression patterns and potential roles in the sheep. Herein, RNA-Seq was used to detect reproduction-related differentially expressed lncRNAs (DELs) and mRNAs (DEGs) in the follicular phase (FT) FecBBB (MM) and FecB++ (ww) genotypes of Small Tail Han (STH) sheep thyroids. Overall, 29 DELs and 448 DEGs in thyroid between MM and ww sheep were screened. Moreover, GO and KEGG enrichment analysis showed that targets of DELs and DEGs were annotated in biological transitions, such as cell cycle, oocyte meiosis and methylation, which in turn affect reproductive performance in sheep. In addition, we constructed co-expression and networks of lncRNAs-mRNAs. Specifically, XLOC_075176 targeted MYB, XLOC_014695 targeted VCAN, 106991527 targeted CASR, XLOC_075176 targeted KIFC1, XLOC_360232 targeted BRCA2. All these differential lncRNAs and mRNAs expression profiles in the thyroid provide a new resource for elucidating the regulatory mechanism underlying STH sheep prolificacy.
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Affiliation(s)
- Cheng Chang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (C.C.); (X.H.); (R.D.); (X.W.)
- College of Animal Science, Shanxi Agricultural University, Jinzhong 030801, China;
| | - Xiaoyun He
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (C.C.); (X.H.); (R.D.); (X.W.)
| | - Ran Di
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (C.C.); (X.H.); (R.D.); (X.W.)
| | - Xiangyu Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (C.C.); (X.H.); (R.D.); (X.W.)
| | - Miaoceng Han
- College of Animal Science, Shanxi Agricultural University, Jinzhong 030801, China;
| | - Chen Liang
- College of Animal Science, Shanxi Agricultural University, Jinzhong 030801, China;
- Correspondence: (C.L.); (M.C.)
| | - Mingxing Chu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (C.C.); (X.H.); (R.D.); (X.W.)
- Correspondence: (C.L.); (M.C.)
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