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Rashad DEM, Ibrahim S, El-Sokary MMM, Mahmoud KGM, Abou El-Roos MEA, Sosa GAM, Kandiel MMM. Abundance of selected genes implicated in testicular functions in Camelus dromedarius with high and low epididymal semen quality. Biol Reprod 2024; 110:501-508. [PMID: 38145478 DOI: 10.1093/biolre/ioad177] [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] [Received: 08/07/2023] [Revised: 11/25/2023] [Accepted: 12/22/2023] [Indexed: 12/26/2023] Open
Abstract
Studying testicular genes' expression may give key insights into precise regulation of its functions that influence epididymal sperm quality. The current study aimed to investigate the abundance of candidate genes involved in the regulation of testicular functions specially those regulate sperm function (PLA2G4D, SPP1, and CLUAP1), testicular steroidogenic function (ESR1 and AR), materials transport (AQP12B and LCN15), and defense mechanisms (DEFB110, GPX5, SOCS3, and IL6). Therefore, blood samples and testes with epididymis were collected from mature middle-aged (5-10 years) dromedary camels (n = 45) directly prior and after their slaughtering, respectively, during breeding season. Sera were evaluated for testosterone level and testicular biometry was measured with caliper. The epididymal tail semen was evaluated manually. Samples were distinguished based on testosterone level, testicular biometry, as well as epididymal semen features into high and low fertile groups. Total RNA was isolated from testicular tissues and gene expression was done using Quantitative Reverse Transcription Polymerase Chain Reaction (qRT-PCR). Results revealed that testosterone levels were significantly (P < 0.005) higher in camels with good semen quality than those of low quality. There was a significant (P < 0.0001) increase in testicular weight, length, width, thickness, and volume in high fertile than low fertile camels. PLA2G4D, SPP1, CLUAP1, ESR1, AR, AQP12B, LCN15, DEFB110, GPX5, and SOCS3 genes were upregulated (P < 0.001), and IL6 gene was downregulated (P < 0.01) in the testes of high fertile camels compared to the low fertile one. Thus, it could be concluded that examined genes might be valuable monitors of testicular functional status and fertility in dromedary camels.
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Affiliation(s)
- Dina E M Rashad
- Theriogenology Department, Faculty of Veterinary Medicine, Benha University, Benha, Egypt
| | - Sally Ibrahim
- Animal Reproduction and Artificial Insemination Department, Veterinary Research Institute, National Research Centre, Dokki, Giza, Egypt
| | - Mohamed M M El-Sokary
- Theriogenology Department, Faculty of Veterinary Medicine, Benha University, Benha, Egypt
| | - Karima Gh M Mahmoud
- Animal Reproduction and Artificial Insemination Department, Veterinary Research Institute, National Research Centre, Dokki, Giza, Egypt
| | | | - Gamal A M Sosa
- Theriogenology Department, Faculty of Veterinary Medicine, Benha University, Benha, Egypt
| | - Mohamed M M Kandiel
- Theriogenology Department, Faculty of Veterinary Medicine, Benha University, Benha, Egypt
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PRM1 Gene Expression and Its Protein Abundance in Frozen-Thawed Spermatozoa as Potential Fertility Markers in Breeding Bulls. Vet Sci 2022; 9:vetsci9030111. [PMID: 35324839 PMCID: PMC8951773 DOI: 10.3390/vetsci9030111] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Revised: 02/22/2022] [Accepted: 02/25/2022] [Indexed: 12/04/2022] Open
Abstract
Functional genes and proteins in sperm play an essential role in bulls’ reproductive processes. They are more accurate in determining bull fertility than conventional semen quality tests. Protamine-1 (PRM1) is a gene or protein crucial for packaging and protecting sperm DNA until fertilization affects normal sperm function. This study analyzes the genes and proteins potential from PRM1 as fertility markers for different breeds of bulls utilized in the artificial insemination programs, expected to be an accurate tool in interpreting bull fertility in Indonesia. This study used Limousin, Holstein, and Ongole Grade bulls divided into two groups based on fertility, high-fertility (HF) and low fertility (LF). The semen quality assessment included progressive motility (computer-assisted semen analysis), viability (eosin-nigrosine), and plasma membrane integrity (HOS test). Sperm DNA fragmentation (SDF) was assessed using the acridine orange staining and the Halomax test. Sperm PRM deficiency was evaluated with the chromomycin A3 method. Moreover, PRM1 gene expression was measured using qRT-PCR, and the PRM1 protein abundance was measured with the enzyme immunoassay method. Semen quality values, relative expression of PRM1 gene, and quantity of PRM1 protein were significantly higher (p < 0.05) in HF bulls than in LF bulls. The SDF and PRM deficiency values in LF bulls were significantly higher (p < 0.05) than HF bulls. Additionally, PRM1 at the gene and protein levels correlated significantly (p < 0.01) with fertility. Therefore, PRM1 is a potential candidate for fertility markers in bulls in Indonesia.
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Pardede BP, Maulana T, Kaiin EM, Agil M, Karja NWK, Sumantri C, Supriatna I. The potential of sperm bovine protamine as a protein marker of semen production and quality at the National Artificial Insemination Center of Indonesia. Vet World 2021; 14:2473-2481. [PMID: 34840468 PMCID: PMC8613797 DOI: 10.14202/vetworld.2021.2473-2481] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Accepted: 08/05/2021] [Indexed: 11/24/2022] Open
Abstract
Background and Aim: Protamine (PRM) is the major protein in the sperm nucleus and plays an essential role in its normal function. Moreover, PRM has great potential as a protein marker of semen production and quality. This study aimed to assess the potential of sperm bovine PRM as a protein marker of semen production and quality in bulls at the National Artificial Insemination (AI) Center of Indonesia. Materials and Methods: The semen production capacity of each bull was collected from frozen semen production data at the Singosari AI Center for 6 months, and was then divided into two groups (high and low). A total of 440 frozen semen straws from six Limousin (LIM), six Friesian Holstein (FH), six Peranakan Ongole (PO), and four Aceh bulls aged 4-5 years were used in the study. The frozen semen was used to measure the concentration of PRM1, PRM2, and PRM3 using the enzyme immunoassay method. The frozen semen was also used to assess the quality of the semen, including progressive motility (PM) through computer-assisted semen analysis, sperm viability through eosin–nigrosin analysis, and the DNA fragmentation index through Acridine Orange staining. Results: PRM1 was significantly higher in all bull breeds included in the study (p<0.00), followed by PRM2 (p<0.00) and PRM3 (p<0.00). PRM1 significantly affected semen production in LIM, FH, PO, and Aceh bulls (p<0.05). Moreover, PRM2 significantly affected semen production only in FH and Aceh bulls (p<0.05), whereas PRM3 affected this parameter in PO and Aceh bulls exclusively (p<0.05). Consistently and significantly, PRM1 was positively correlated with the PM and viability of sperm and negatively associated with its DNA fragmentation in LIM, FH, PO, and Aceh bulls (p<0.05; p<0.01). The correlation analysis between PRM2 and PRM3 and semen quality parameters varied across all bull breeds; some were positively and negatively correlated (p<0.05; p<0.01), and some were not correlated at all. Conclusion: PRM1 has excellent potential as a protein marker of semen production and quality in bulls at the National AI Center of Indonesia.
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Affiliation(s)
- Berlin Pandapotan Pardede
- Reproductive Biology Study Program, Faculty of Veterinary Medicine, IPB University, Dramaga, Bogor 16680, Indonesia
| | - Tulus Maulana
- Animal Reproduction Biotechnology Research Group, Research Center for Biotechnology, Indonesian Institute of Sciences, West Java, Indonesia
| | - Ekayanti Mulyawati Kaiin
- Animal Reproduction Biotechnology Research Group, Research Center for Biotechnology, Indonesian Institute of Sciences, West Java, Indonesia
| | - Muhammad Agil
- Department of Veterinary Clinic, Reproduction, and Pathology, Faculty of Veterinary Medicine, IPB University, Dramaga, Bogor 16680, Indonesia
| | - Ni Wayan Kurniani Karja
- Department of Veterinary Clinic, Reproduction, and Pathology, Faculty of Veterinary Medicine, IPB University, Dramaga, Bogor 16680, Indonesia
| | - Cece Sumantri
- Department of Animal Production and Technology, Faculty of Animal Science, IPB University, Dramaga, Bogor 16680, Indonesia
| | - Iman Supriatna
- Department of Veterinary Clinic, Reproduction, and Pathology, Faculty of Veterinary Medicine, IPB University, Dramaga, Bogor 16680, Indonesia
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Gundogan GI, Aktas A. Immunolocalization of Fertilin β, IZUMO1, and P34H in Ram Spermatozoa. Biopreserv Biobank 2021; 19:470-482. [PMID: 33956503 DOI: 10.1089/bio.2021.0006] [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] [Indexed: 01/13/2023] Open
Abstract
According to various reports, current methods of sperm freezing destroy the integrity of the sperm plasma membrane and acrosome. This study aimed to determine the changes in the existence and location of three proteins, namely fertilin β, IZUMO1, and P34H, in ram spermatozoa. By using frozen-thawed spermatozoa, ejaculated fresh spermatozoa, and testicular and epididymal spermatozoa (obtained from caput, corpus, and caudal regions), the localizations of the mentioned proteins were performed using signal labeling with indirect immunofluorescence, and the quantification of these proteins was compared using Western blot analyses. Moreover, protein localization and signal labeling in fresh and frozen-thawed spermatozoa subjected to in vitro capacitation and acrosome reaction were compared. Using chlortetracycline (CTC) staining, as expected, it was detected that after incubating for 4 hours under capacitating conditions related to the control sample (0 hour), capacitated and acrosome-reacted sperm were increased (p < 0.001). Frozen-thawed samples had a lower density and expression than the ejaculate samples. Expression was not obtained, except for IZUMO1, from samples that underwent in vitro capacitation/acrosome reactions. Expression of IZUMO1 was seen as an increasing band formation from the equatorial region through the acrosome, after in vitro capacitation. However, after the acrosome reaction, the band formation was only on the equatorial region. Region-specific differences of proteins at the kDa level were obtained using Western blot analysis and possible isoforms specific to ram spermatozoa or proteins with similar epitopes were expressed. Considering the changes in surface proteins in frozen-thawed sperm, it is suggested that fertilin β and P34H can be used as fertility or freezability markers.
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Affiliation(s)
- Gul Ipek Gundogan
- Department of Histology and Embryology, Faculty of Medicine, Istanbul Yeni Yuzyıl University, Istanbul, Turkey
| | - Abit Aktas
- Department of Histology and Embryology, Faculty of Veterinary Medicine, Istanbul University-Cerrahpasa, Istanbul, Turkey
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Khan IM, Cao Z, Liu H, Khan A, Rahman SU, Khan MZ, Sathanawongs A, Zhang Y. Impact of Cryopreservation on Spermatozoa Freeze-Thawed Traits and Relevance OMICS to Assess Sperm Cryo-Tolerance in Farm Animals. Front Vet Sci 2021; 8:609180. [PMID: 33718466 PMCID: PMC7947673 DOI: 10.3389/fvets.2021.609180] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Accepted: 02/01/2021] [Indexed: 12/12/2022] Open
Abstract
Sperm cryopreservation is a powerful tool for the livestock breeding program. Several technical attempts have been made to enhance the efficiency of spermatozoa cryopreservation in different farm animal species. However, it is well-recognized that mammalian spermatozoa are susceptible to cryo-injury caused by cryopreservation processes. Moreover, the factors leading to cryo-injuries are complicated, and the cryo-damage mechanism has not been methodically explained until now, which directly influences the quality of frozen–thawed spermatozoa. Currently, the various OMICS technologies in sperm cryo-biology have been conducted, particularly proteomics and transcriptomics studies. It has contributed while exploring the molecular alterations caused by cryopreservation, identification of various freezability markers and specific proteins that could be added to semen diluents before cryopreservation to improve sperm cryo-survival. Therefore, understanding the cryo-injury mechanism of spermatozoa is essential for the optimization of current cryopreservation processes. Recently, the application of newly-emerged proteomics and transcriptomics technologies to study the effects of cryopreservation on sperm is becoming a hotspot. This review detailed an updated overview of OMICS elements involved in sperm cryo-tolerance and freeze-thawed quality. While also detailed a mechanism of sperm cryo-injury and utilizing OMICS technology that assesses the sperm freezability potential biomarkers as well as the accurate classification between the excellent and poor freezer breeding candidate.
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Affiliation(s)
- Ibrar Muhammad Khan
- Anhui Provincial Laboratory of Local Livestock and Poultry Genetical Resource Conservation and Breeding, College of Animal Science and Technology, Anhui Agricultural University, Hefei, China
| | - Zubing Cao
- Anhui Provincial Laboratory of Local Livestock and Poultry Genetical Resource Conservation and Breeding, College of Animal Science and Technology, Anhui Agricultural University, Hefei, China
| | - Hongyu Liu
- Anhui Provincial Laboratory of Local Livestock and Poultry Genetical Resource Conservation and Breeding, College of Animal Science and Technology, Anhui Agricultural University, Hefei, China
| | - Adnan Khan
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agriculture Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Sajid Ur Rahman
- Key Laboratory of Animal Parasitology of Ministry of Agriculture, Laboratory of Quality and Safety Risk Assessment for Animal Products on Biohazards (Shanghai) of Ministry of Agricultural Sciences, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Muhammad Zahoor Khan
- State Key Laboratory of Animal Nutrition, Beijing Engineering Technology Research Center of Raw Milk Quality and Safety Control, College of Animal Science and Technology, China Agriculture University, Beijing, China
| | - Anucha Sathanawongs
- Department of Veterinary Biosciences and Veterinary Public Health, Faculty of Veterinary Medicine, Chiang Mai University, Chiang Mai, Thailand
| | - Yunhai Zhang
- Anhui Provincial Laboratory of Local Livestock and Poultry Genetical Resource Conservation and Breeding, College of Animal Science and Technology, Anhui Agricultural University, Hefei, China
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Pardede BP, Agil M, Supriatna I. Protamine and other proteins in sperm and seminal plasma as molecular markers of bull fertility. Vet World 2020; 13:556-562. [PMID: 32367964 PMCID: PMC7183474 DOI: 10.14202/vetworld.2020.556-562] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2019] [Accepted: 02/14/2020] [Indexed: 12/12/2022] Open
Abstract
Fertility is the most important aspect in the efforts to increase livestock populations. Protamine and various proteins in sperm and seminal plasma are the results of the molecular analysis which can be used as a marker of fertility. Each of the proteins plays an important role in the normal function of sperm, starting from the formation of sperm structure, motility, capacitation, cell protection, acrosome reactions, successful fertilization, egg activation, and embryonic development. Finally, these molecular components can be a marker of fertility and can help to diagnose the cases of infertility/subfertility in livestock in the field.
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Affiliation(s)
- Berlin Pandapotan Pardede
- Reproductive Biology Study Program, Faculty of Veterinary Medicine, IPB University, Bogor, Indonesia
| | - Muhammad Agil
- Department of Veterinary Clinic, Reproduction and Pathology, Division of Reproduction and Obstetric, Faculty of Veterinary Medicine, IPB University, Bogor, Indonesia
| | - Iman Supriatna
- Department of Veterinary Clinic, Reproduction and Pathology, Division of Reproduction and Obstetric, Faculty of Veterinary Medicine, IPB University, Bogor, Indonesia
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8
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Câmara DR, Kastelic JP, Thundathil JC. Role of the Na +/K +-ATPase ion pump in male reproduction and embryo development. Reprod Fertil Dev 2018; 29:1457-1467. [PMID: 27456939 DOI: 10.1071/rd16091] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Accepted: 06/19/2016] [Indexed: 12/18/2022] Open
Abstract
Na+/K+-ATPase was one of the first ion pumps studied because of its importance in maintaining osmotic and ionic balances between intracellular and extracellular environments, through the exchange of three Na+ ions out and two K+ ions into a cell. This enzyme, which comprises two main subunits (α and β), with or without an auxiliary polypeptide (γ), can have specific biochemical properties depending on the expression of associated isoforms (α1β1 and/or α2β1) in the cell. In addition to the importance of Na+/K+-ATPase in ensuring the function of many tissues (e.g. brain, heart and kidney), in the reproductive tract this protein is essential for embryo development because of its roles in blastocoel formation and embryo hatching. In the context of male reproduction, the discovery of a very specific subunit (α4), apparently restricted to male germ cells, only expressed after puberty and able to influence sperm function (e.g. motility and capacitation), opened a remarkable field for further investigations regarding sperm biology. Therefore, the present review focuses on the importance of Na+/K+-ATPase on male reproduction and embryo development.
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Affiliation(s)
- D R Câmara
- Faculdade de Medicina Veterinária, Universidade Federal de Alagoas, Fazenda São Luiz, s/n, Zona Rural do Município de Viçosa, Viçosa-AL, CEP: 57700-000, Brazil
| | - J P Kastelic
- Department of Production Animal Health, Faculty of Veterinary Medicine, University of Calgary, 3330 Hospital Dr., NW, Calgary, AB T2N 4N1, Canada
| | - J C Thundathil
- Department of Production Animal Health, Faculty of Veterinary Medicine, University of Calgary, 3330 Hospital Dr., NW, Calgary, AB T2N 4N1, Canada
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9
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Genetic correlations between yield traits or days open measured in cows and semen production traits measured in bulls. Animal 2017; 12:2027-2031. [PMID: 29268810 DOI: 10.1017/s1751731117003470] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
We used a bivariate animal model to investigate the genetic correlations between yield traits or days open (DO) as characters measured in cows and semen production traits as characters measured in bulls. Lactation records of 305-day milk, fat, and protein yields, and DO, from 386 809 first-lactation Holstein cows in Hokkaido, Japan, that calved between 2008 and 2014 were used. Semen production records were collected between 2005 and 2014 and included volume per ejaculate (VOL), sperm concentration (CON), number of sperm per ejaculate (NUM), progressive motility index of sperm (MOT), and MOT after freeze-thawing (A-MOT). Number of sperm per ejaculate was log-transformed into a NUM score (NUMS). A total of 30 373 semen production records from 1196 bulls were obtained. The pedigree file used for analysing the records was involving 885 345 animals. Heritability was estimated for VOL (0.42), CON (0.12), NUMS (0.37), MOT (0.08), and A-MOT (0.11). Weak and negative genetic correlations were recorded between yield traits measured in cows and VOL, CON or NUMS measured in bulls. Moderate and negative genetic correlations were obtained between DO and MOT (-0.42) or A-MOT (-0.43). Selection focused on MOT or A-MOT measured in bulls may therefore improve DO measured in cows.
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Pitia AM, Uchiyama K, Sano H, Kinukawa M, Minato Y, Sasada H, Kohsaka T. Functional insulin-like factor 3 (INSL3) hormone-receptor system in the testes and spermatozoa of domestic ruminants and its potential as a predictor of sire fertility. Anim Sci J 2016; 88:678-690. [PMID: 27592693 DOI: 10.1111/asj.12694] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Revised: 05/31/2016] [Accepted: 06/26/2016] [Indexed: 11/30/2022]
Abstract
Insulin-like factor 3 (INSL3) is essential for fetal testis descent, and has been implicated in the testicular and sperm functions in adult males; however, similar functions in domestic ruminants remain largely unknown. This study investigated the functional INSL3 hormone-receptor system in adult ruminant testes and spermatozoa, and explored its potential to diagnose the fertility of sires. Testes and spermatozoa were obtained from fertile bulls, rams and he-goats, whereas subfertile testes and spermatozoa were obtained only from bulls. As expected, INSL3 was visualized in Leydig cells, while we clearly demonstrated that the functional receptor, relaxin family peptide receptor 2 (RXFP2), enabling INSL3 to bind was identified in testicular germ cells and in the sperm equatorial segment of bulls, rams and he-goats. In comparison to fertile bulls, the percentage of INSL3- and RXFP2-expressing cells and their expression levels per cell were significantly reduced in the testes of subfertile bulls. In addition, the population of INSL3-binding spermatozoa was also significantly reduced in the semen of subfertile bulls. These results provide evidence for a functional INSL3 hormone-receptor system operating in ruminant testes and spermatozoa, and its potential to predict subfertility in sires.
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Affiliation(s)
- Ali M Pitia
- Division of Animal Resource Production, United Graduate School of Agricultural Science, Gifu University, Gifu, Japan.,Laboratory of Animal Reproduction and Physiology, Faculty of Agriculture, Shizuoka University, Shizuoka, Japan
| | - Kyoko Uchiyama
- Division of Animal Reproduction, Maebashi Institute of Animal Science, Livestock Improvement Association of Japan (LIAJ), Maebashi, Japan
| | - Hiroaki Sano
- Department of Animal Science, Faculty of Agriculture, Iwate University, Morioka, Japan
| | - Masashi Kinukawa
- Division of Animal Reproduction, Maebashi Institute of Animal Science, Livestock Improvement Association of Japan (LIAJ), Maebashi, Japan
| | - Yoshiaki Minato
- Division of Animal Reproduction, Maebashi Institute of Animal Science, Livestock Improvement Association of Japan (LIAJ), Maebashi, Japan
| | - Hiroshi Sasada
- Laboratory of Animal Reproduction, School of Veterinary Medicine, Kitasato University, Towada, Japan
| | - Tetsuya Kohsaka
- Division of Animal Resource Production, United Graduate School of Agricultural Science, Gifu University, Gifu, Japan.,Laboratory of Animal Reproduction and Physiology, Faculty of Agriculture, Shizuoka University, Shizuoka, Japan
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Choi JW, Choi BH, Lee SH, Lee SS, Kim HC, Yu D, Chung WH, Lee KT, Chai HH, Cho YM, Lim D. Whole-Genome Resequencing Analysis of Hanwoo and Yanbian Cattle to Identify Genome-Wide SNPs and Signatures of Selection. Mol Cells 2015; 38:466-73. [PMID: 26018558 PMCID: PMC4443289 DOI: 10.14348/molcells.2015.0019] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2015] [Revised: 03/20/2015] [Accepted: 03/13/2015] [Indexed: 01/11/2023] Open
Abstract
Over the last 30 years, Hanwoo has been selectively bred to improve economically important traits. Hanwoo is currently the representative Korean native beef cattle breed, and it is believed that it shared an ancestor with a Chinese breed, Yanbian cattle, until the last century. However, these two breeds have experienced different selection pressures during recent decades. Here, we whole-genome sequenced 10 animals each of Hanwoo and Yanbian cattle (20 total) using the Illumina HiSeq 2000 sequencer. A total of approximately 3.12 and 3.07 billion sequence reads were mapped to the bovine reference sequence assembly (UMD 3.1) at an average of approximately 10.71- and 10.53-fold coverage for Hanwoo and Yanbian cattle, respectively. A total of 17,936,399 single nucleotide polymorphisms (SNPs) were yielded, of which 22.3% were found to be novel. By annotating the SNPs, we further retrieved numerous nonsynonymous SNPs that may be associated with traits of interest in cattle. Furthermore, we performed whole-genome screening to detect signatures of selection throughout the genome. We located several promising selective sweeps that are potentially responsible for economically important traits in cattle; the PPP1R12A gene is an example of a gene that potentially affects intramuscular fat content. These discoveries provide valuable genomic information regarding potential genomic markers that could predict traits of interest for breeding programs of these cattle breeds.
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Affiliation(s)
- Jung-Woo Choi
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, Rural Development Administration, Suwon 441-706,
Korea
| | - Bong-Hwan Choi
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, Rural Development Administration, Suwon 441-706,
Korea
| | - Seung-Hwan Lee
- Division of Animal and Dairy Science, Chung Nam National University, Daejeon 305-764,
Korea
| | - Seung-Soo Lee
- Animal Genetic and Breeding Division, National Institute of Animal Science, Cheon-An 331-808,
Korea
| | - Hyeong-Cheol Kim
- Hanwoo Experiment Station, National Institute of Animal Science, RDA, Pyeongchang 232-950,
Korea
| | - Dayeong Yu
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, Rural Development Administration, Suwon 441-706,
Korea
| | - Won-Hyong Chung
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, Rural Development Administration, Suwon 441-706,
Korea
| | - Kyung-Tai Lee
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, Rural Development Administration, Suwon 441-706,
Korea
| | - Han-Ha Chai
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, Rural Development Administration, Suwon 441-706,
Korea
| | - Yong-Min Cho
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, Rural Development Administration, Suwon 441-706,
Korea
| | - Dajeong Lim
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, Rural Development Administration, Suwon 441-706,
Korea
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