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Kang M, Ahn B, Youk S, Jeon H, Soundarajan N, Cho ES, Park W, Park C. Individual and population diversity of 20 representative olfactory receptor genes in pigs. Sci Rep 2023; 13:18668. [PMID: 37907519 PMCID: PMC10618239 DOI: 10.1038/s41598-023-45784-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Accepted: 10/24/2023] [Indexed: 11/02/2023] Open
Abstract
Understanding the influence of genetic variations in olfactory receptor (OR) genes on the olfaction-influenced phenotypes such as behaviors, reproduction, and feeding is important in animal biology. However, our understanding of the complexity of the OR subgenome is limited. In this study, we analyzed 1120 typing results of 20 representative OR genes belonging to 13 OR families on 14 pig chromosomes from 56 individuals belonging to seven different breeds using a sequence-based OR typing method. We showed that the presence of copy number variations, conservation of locus-specific diversity, abundance of breed-specific alleles, presence of a loss-of-function allele, and low-level purifying selection in pig OR genes could be common characteristics of OR genes in mammals. The observed nucleotide sequence diversity of pig ORs was higher than that of dogs. To the best of our knowledge, this is the first report on the individual- or population-level characterization of a large number of OR family genes in livestock species.
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Affiliation(s)
- Mingue Kang
- Department of Stem Cell and Regenerative Biotechnology, Konkuk University, Seoul, 05029, Republic of Korea
| | - Byeongyong Ahn
- Department of Stem Cell and Regenerative Biotechnology, Konkuk University, Seoul, 05029, Republic of Korea
| | - Seungyeon Youk
- Department of Stem Cell and Regenerative Biotechnology, Konkuk University, Seoul, 05029, Republic of Korea
| | - Hyoim Jeon
- Department of Stem Cell and Regenerative Biotechnology, Konkuk University, Seoul, 05029, Republic of Korea
| | | | - Eun-Seok Cho
- Rural Development Administration, National Institute of Animal Science, Wanju, 55365, Republic of Korea
| | - Woncheoul Park
- Rural Development Administration, National Institute of Animal Science, Wanju, 55365, Republic of Korea
| | - Chankyu Park
- Department of Stem Cell and Regenerative Biotechnology, Konkuk University, Seoul, 05029, Republic of Korea.
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Tao D, Liu J, Li Q, Jiang Y, Xu B, Khazalwa EM, Gong P, Xu J, Ma Y, Ruan J, Niu L, Xie S. A Simple, Affordable, and Rapid Visual CRISPR-Based Field Test for Sex Determination of Earlier Porcine Embryos and Pork Products. Mol Biotechnol 2023; 65:263-272. [PMID: 35840848 DOI: 10.1007/s12033-022-00532-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2022] [Accepted: 06/29/2022] [Indexed: 01/18/2023]
Abstract
Sex selection technologies have immensely impacted swine production globally. Conventional earlier embryo sex identification methods require professional technicians and sophisticated laboratory instruments. Rapid on-site gender identification of porcine embryos and pork products remains challenging. In this study, we developed a CRISPR/Cas12a-based fluorescence visualization point-of-care sex determination test that is rapid, accurate and easy to implement on-site. The CRISPR/Cas12a assay coupled with either the polymerase chain reaction (PCR) or loop-mediated isothermal amplification (LAMP) employs precisely designed primers and single-guide RNAs targeting the sex-determining region Y (SRY) and the zinc finger protein X-linked (ZFX) genes. PCR and LAMP amplicons were cleaved with the subsequent generation of fluorescing products detectable with portable blue and ultraviolet light transilluminators. Approximately two copies per microliter of the ZFX and SRY genes were detected using the RApid VIsual CRISPR (RAVI-CRISPR) assay. This method is a sensitive, inexpensive, versatile, and point-of-care test. The technology has other potential applications like determining the sex of diverse livestock species, detecting livestock disease-causing pathogens and evaluating the quality of meat products.
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Affiliation(s)
- Dagang Tao
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education & Key Lab of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
| | - Jiajia Liu
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, People's Republic of China
| | - Qiushi Li
- College of Biological Engineering and Food Science, Hubei University of Technology, Wuhan, 430070, People's Republic of China
| | - Yu Jiang
- Yangshan Customs, Shanghai, 201306, People's Republic of China
| | - Bingrong Xu
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education & Key Lab of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
| | | | - Ping Gong
- Institute of Animal Husbandry and Veterinary, Wuhan Academy of Agricultural Science, Wuhan, 430208, People's Republic of China
| | - Jing Xu
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education & Key Lab of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
| | - Yunlong Ma
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education & Key Lab of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
| | - Jinxue Ruan
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education & Key Lab of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China.,Hubei Hongshan Laboratory, Frontiers Science Center for Animal Breeding and Sustainable Production, Wuhan, 430070, People's Republic of China
| | - Lili Niu
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, People's Republic of China.
| | - Shengsong Xie
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education & Key Lab of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China. .,Hubei Hongshan Laboratory, Frontiers Science Center for Animal Breeding and Sustainable Production, Wuhan, 430070, People's Republic of China.
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Mishra A, Dhali A, Reddy IJ, Kolte AP. Sexing of pre-implantation ovine embryos through polymerase chain reaction-based amplification of GAPDH, SRY and AMEL genes. Reprod Domest Anim 2020; 55:885-892. [PMID: 32379910 DOI: 10.1111/rda.13699] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Accepted: 04/24/2020] [Indexed: 11/27/2022]
Abstract
The ability to identify the sex of embryo and control of sex ratio has a great commercial importance to livestock industry. Prediction of embryonic sex could be useful in the management decisions of sex selection in breeding programs. Several methods have been attempted to determine the sex but the polymerase chain reaction (PCR)-based sexing method is generally favoured, as it is cost effective, simple and reliable. The aim of the present study was to identify sex of sheep embryos produced in vitro through amplification of glyceraldehyde 3-phosphate dehydrogenase (GAPDH), sex-determining region Y (SRY) and amelogenin genes present in genomic DNA (gDNA) of embryos through PCR. To avoid false interpretation of the result by no amplification of SRY in female embryos, a duplex PCR was approached to amplify combinedly SRY and GAPDH genes. Sex-specific blood was used in PCR as positive control. In vitro sheep embryos were produced as per standardized protocol of laboratory. Sexing of sex-specific blood and in vitro produced embryos were approached though PCR to amplify the respective genes using gDNA present in the sample without its traditional isolation. The accuracy of sex prediction for embryos was 100% by this procedure.
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Affiliation(s)
- Ashish Mishra
- ICAR-National Institute of Animal Nutrition and Physiology, Bangalore, India
| | - Arindam Dhali
- ICAR-National Institute of Animal Nutrition and Physiology, Bangalore, India
| | - Ippala J Reddy
- ICAR-National Institute of Animal Nutrition and Physiology, Bangalore, India
| | - Atul P Kolte
- ICAR-National Institute of Animal Nutrition and Physiology, Bangalore, India
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Belousova I, Ershov N, Pavlushin S, Ilinsky Y, Martemyanov V. Molecular sexing of Lepidoptera. JOURNAL OF INSECT PHYSIOLOGY 2019; 114:53-56. [PMID: 30776424 DOI: 10.1016/j.jinsphys.2019.02.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2018] [Revised: 02/14/2019] [Accepted: 02/14/2019] [Indexed: 06/09/2023]
Abstract
We developed a universal method of Lepidoptera molecular sexing. The method is based on comparing the number of copies of the same gene in different sexes. Males of the majority of lepidopteran species have two Z chromosomes, whereas females have only one Z chromosome. Correspondingly, the number of copies of each gene located on this chromosome differs by two times between males and females. For quantitative estimation, we used qPCR. Via multiple alignment of the kettin (a Z chromosome gene) nucleotide sequences, we detected the most conserved fragment and designed primers with broad interspecies specificity for Lepidoptera. Using these primers, we successfully determined the sex of three lepidopteran species belonging to different superfamilies. The developed method is a simple, cost-effective and high-throughput technique for routine sexing. The sex of lepidopteran individuals can be examined at any developmental stage.
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Affiliation(s)
- Irina Belousova
- Institute of Systematics and Ecology of Animals SB RAS, Frunze Str. 11, Novosibirsk 630091 Russia.
| | - Nikita Ershov
- Institute of Cytology and Genetics SB RAS, Prospekt Lavrentyeva 10, Novosibirsk 630090, Russia
| | - Sergey Pavlushin
- Institute of Systematics and Ecology of Animals SB RAS, Frunze Str. 11, Novosibirsk 630091 Russia
| | - Yury Ilinsky
- Institute of Cytology and Genetics SB RAS, Prospekt Lavrentyeva 10, Novosibirsk 630090, Russia; Novosibirsk State University, Pirogova Str. 2, Novosibirsk 630090, Russia; School of Life Sciences Immanuel Kant Baltic Federal University, Nevskogo Str. 14, Kaliningrad 236016, Russia
| | - Vyacheslav Martemyanov
- Institute of Systematics and Ecology of Animals SB RAS, Frunze Str. 11, Novosibirsk 630091 Russia; Biological Institute, National Research Tomsk State University, Lenin Ave. 36, Tomsk 634050, Russia
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Literman R, Badenhorst D, Valenzuela N. qPCR-based molecular sexing by copy number variation in rRNA genes and its utility for sex identification in soft-shell turtles. Methods Ecol Evol 2014. [DOI: 10.1111/2041-210x.12228] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Robert Literman
- Department of Ecology, Evolution and Organismal Biology; Iowa State University; 251 Bessey Hall Ames IA 50011 USA
| | - Daleen Badenhorst
- Department of Ecology, Evolution and Organismal Biology; Iowa State University; 251 Bessey Hall Ames IA 50011 USA
| | - Nicole Valenzuela
- Department of Ecology, Evolution and Organismal Biology; Iowa State University; 251 Bessey Hall Ames IA 50011 USA
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Rovatsos M, Altmanová M, Pokorná M, Kratochvíl L. CONSERVED SEX CHROMOSOMES ACROSS ADAPTIVELY RADIATEDANOLISLIZARDS. Evolution 2014; 68:2079-85. [DOI: 10.1111/evo.12357] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2013] [Accepted: 01/08/2014] [Indexed: 12/17/2022]
Affiliation(s)
- Michail Rovatsos
- Department of Ecology; Faculty of Science; Charles University in Prague; Viničná 7, 12844 Praha 2 Czech Republic
| | - Marie Altmanová
- Department of Ecology; Faculty of Science; Charles University in Prague; Viničná 7, 12844 Praha 2 Czech Republic
| | - Martina Pokorná
- Department of Ecology; Faculty of Science; Charles University in Prague; Viničná 7, 12844 Praha 2 Czech Republic
- Department of Vertebrate Evolutionary Biology and Genetics; Institute of Animal Physiology and Genetics; Academy of Sciences of the Czech Republic; Rumburská 89 277 21 Liběchov Czech Republic
| | - Lukáš Kratochvíl
- Department of Ecology; Faculty of Science; Charles University in Prague; Viničná 7, 12844 Praha 2 Czech Republic
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