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Vieira JIG, Braga LG, Chud TCS, Ferreira PH, Guimarães SEF, Martins MF, do Carmo Panetto JC, Machado MA, Silva DBDS, Bonafé CM, Magalhães AFB, da Silva MVGB, Verardo LL. Resequencing of Brazilian locally adapted cattle breeds revealed variants in candidate genes and transcription factors for meat fatty acid profile. J Anim Breed Genet 2024; 141:628-642. [PMID: 38686591 DOI: 10.1111/jbg.12869] [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: 07/25/2023] [Revised: 04/15/2024] [Accepted: 04/19/2024] [Indexed: 05/02/2024]
Abstract
The beef cattle industry has experienced a shift driven by a market demand for healthier meat, cost efficiency and environmental sustainability in recent years. Consequently, there has been a growing focus on the fatty acids content and functions of meat in cattle breeding programmes. Besides, a deeper understanding of the biological mechanisms influencing the expression of different phenotypes related to fatty acid profiles is crucial. In this study, we aimed to identify Single-Nucleotide Variants (SNV) and Insertion/Deletion (InDels) DNA variants in candidate genes related to fatty acid profiles described in genomic, transcriptomic and proteomic studies conducted in beef cattle breeds. Utilizing whole-genome re-sequencing data from Brazilian locally adapted bovine breeds, namely Caracu and Pantaneiro, we identified SNVs and InDels associated with 23,947 genes. From these, we identified 318 candidate genes related to fatty acid profiles that contain variants. Subsequently, we select only genes with SNVs and InDels in their promoter, 5' UTR and coding region. Through the gene-biological process network, approximately 19 genes were highlighted. Furthermore, considering the studied trait and a literature review, we selected the main transcription factors (TF). Functional analysis via gene-TF network allowed us to identify the 30 most likely candidate genes for meat fatty acid profile in cattle. LIPE, MFSD2A and SREBF1 genes were highlighted in networks due to their biological importance. Further dissection of these genes revealed 15 new variants found in promoter regions of Caracu and Pantaneiro sequences. The gene networks facilitated a better functional understanding of genes and TF, enabling the identification of variants potentially related to the expression of candidate genes for meat fatty acid profiles in cattle.
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Affiliation(s)
| | - Larissa Graciano Braga
- Departamento de Engenharia e Ciências Exatas, Universidade Estadual Paulista, São Paulo, Brazil
| | | | | | | | | | | | | | | | | | | | | | - Lucas Lima Verardo
- Universidade Federal dos Vales Do Jequitinhonha e Mucuri, Diamantina, Minas Gerais, Brazil
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Wang X, Qi Y, Zhu C, Zhou R, Ruo Z, Zhao Z, Liu X, Li S, Zhao F, Wang J, Hu J, Shi B. Variation in the HSL Gene and Its Association with Carcass and Meat Quality Traits in Yak. Animals (Basel) 2023; 13:3720. [PMID: 38067071 PMCID: PMC10705307 DOI: 10.3390/ani13233720] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 11/20/2023] [Accepted: 11/28/2023] [Indexed: 09/10/2024] Open
Abstract
Hormone-sensitive lipase (HSL) is involved in the breakdown of triacylglycerols in adipose tissue, which influences muscle tenderness and juiciness by affecting the intramuscular fat content (IMF). This study analyzed the association between different genotypes and haplotypes of the yak HSL gene and carcass and meat quality traits. We used hybridization pool sequencing to detect exon 2, exon 8, and intron 3 variants of the yak HSL gene and genotyped 525 Gannan yaks via KASP to analyze the effects of the HSL gene variants on the carcass and meat quality traits in yaks. According to the results, the HSL gene is highly expressed in yak adipose tissue. Three single nucleotide polymorphisms (SNPs) were identified, with 2 of them located in the coding region and one in the intron region. Variants in the 2 coding regions resulted in amino acid changes. The population had 3 genotypes of GG, AG, and AA, and individuals with the AA genotype had lower WBSF values (p < 0.05). The H3H3 haplotype combinations could improve meat tenderness by reducing the WBSF values and the cooking loss rate (CLR) (p < 0.05). H1H1 haplotype combinations were associated with the increased drip loss rate (DLR) (p < 0.05). The presence of the H1 haplotype was associated the increased CLR in yaks, while that of the H2 haplotype was associated with the decreased DLR in yaks (p < 0.05). These results demonstrated that the HSL gene may influence the meat quality traits in yaks by affecting the IMF content in muscle tissues. Consequently, the HSL gene can possibly be used as a biomarker for improving the meat quality traits in yaks in the future.
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Affiliation(s)
- Xiangyan Wang
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China; (X.W.); (C.Z.); (R.Z.); (Z.Z.); (X.L.); (S.L.); (F.Z.); (J.W.)
| | - Youpeng Qi
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China; (X.W.); (C.Z.); (R.Z.); (Z.Z.); (X.L.); (S.L.); (F.Z.); (J.W.)
| | - Chune Zhu
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China; (X.W.); (C.Z.); (R.Z.); (Z.Z.); (X.L.); (S.L.); (F.Z.); (J.W.)
| | - Ruifeng Zhou
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China; (X.W.); (C.Z.); (R.Z.); (Z.Z.); (X.L.); (S.L.); (F.Z.); (J.W.)
| | - Zhoume Ruo
- Maqin County Dawu Town Agricultural and Animal Husbandry Technical Service Station, Guoluo Prefecture 814000, China;
| | - Zhidong Zhao
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China; (X.W.); (C.Z.); (R.Z.); (Z.Z.); (X.L.); (S.L.); (F.Z.); (J.W.)
| | - Xiu Liu
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China; (X.W.); (C.Z.); (R.Z.); (Z.Z.); (X.L.); (S.L.); (F.Z.); (J.W.)
| | - Shaobin Li
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China; (X.W.); (C.Z.); (R.Z.); (Z.Z.); (X.L.); (S.L.); (F.Z.); (J.W.)
| | - Fangfang Zhao
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China; (X.W.); (C.Z.); (R.Z.); (Z.Z.); (X.L.); (S.L.); (F.Z.); (J.W.)
| | - Jiqing Wang
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China; (X.W.); (C.Z.); (R.Z.); (Z.Z.); (X.L.); (S.L.); (F.Z.); (J.W.)
| | - Jiang Hu
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China; (X.W.); (C.Z.); (R.Z.); (Z.Z.); (X.L.); (S.L.); (F.Z.); (J.W.)
| | - Bingang Shi
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China; (X.W.); (C.Z.); (R.Z.); (Z.Z.); (X.L.); (S.L.); (F.Z.); (J.W.)
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Qiao Y, Gu M, Zhang Y, Bai Z, Qin Y, Xu Y, Dou X, Han D, Lin G, Wang L, Wang Z, Wang J, Sun Y, Wu Y, Chen R, Zhang Q, Li Q, Wang X, Xu Z, Cong Y, Chen J, Wang Z. Association analysis for SNPs of LIPE and ITGB4 genes with cashmere production performance, body measurement traits and milk production traits in Liaoning cashmere goats. Anim Biotechnol 2023; 34:3827-3836. [PMID: 37428531 DOI: 10.1080/10495398.2023.2230484] [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: 07/11/2023]
Abstract
Liaoning cashmere goat (LCG) is one of the excellent cashmere goat breeds in China. Because of its larger size, better cashmere, and better cashmere production performance, people pay special attention to it. This article mainly studied the relationship between SNP loci of LIPE gene and ITGB4 gene and milk production, cashmere production and body measurement traits of LCGs. We further identified potential SNP loci by PCR-Seq polymorphism detection and gene sequence comparison of LIPE and ITGB4 genes. Further, we use SPSS and SHEsis software to analyze their relationship to production performance. The consequence indicated that CC genotype of LIPE gene T16409C locus was dominant genotype in milk production and cashmere production, while CT genotype of LIPE gene T16409C locus was dominant in body size. The CT genotype of C168T locus of ITGB4 gene is the dominant genotype of body type and cashmere production, while the dominant genotype of milk production is TT genotype. Through joint analysis, in haploid combinations, H1H2:CCCT is the dominant haplotype combination in cashmere fineness. H3H4:TTCT is a dominant haplotype combination of milk production traits and body measurement traits. These dominant genotypes can provide a reliable basis for the study of production performance of LCG.
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Affiliation(s)
- Yanjun Qiao
- College of Animal Science & Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Ming Gu
- College of Animal Science & Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Yu Zhang
- College of Animal Science & Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Zhixian Bai
- College of Animal Science & Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Yuting Qin
- College of Animal Science & Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Yanan Xu
- College of Animal Science & Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Xingtang Dou
- Liaoning Province Modern Agricultural Production Base Construction Engineering Center, Liaoyang, China
| | - Di Han
- Liaoning Province Modern Agricultural Production Base Construction Engineering Center, Liaoyang, China
| | - Guangyu Lin
- Liaoning Province Modern Agricultural Production Base Construction Engineering Center, Liaoyang, China
| | - Lingling Wang
- Liaoning Province Modern Agricultural Production Base Construction Engineering Center, Liaoyang, China
| | - Zhanhong Wang
- Liaoning Province Modern Agricultural Production Base Construction Engineering Center, Liaoyang, China
| | - Jiaming Wang
- Liaoning Province Modern Agricultural Production Base Construction Engineering Center, Liaoyang, China
| | - Yinggang Sun
- College of Animal Science & Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Yanzhi Wu
- College of Animal Science & Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Rui Chen
- College of Animal Science & Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Qiu Zhang
- College of Animal Science & Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Qian Li
- College of Animal Science & Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Xiaowei Wang
- College of Animal Science & Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Zhiguo Xu
- Dalian Modern Agricultural Production Development Service Center, Dalian, China
| | - Yuyan Cong
- College of Animal Science & Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Jing Chen
- College of Animal Science & Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Zeying Wang
- College of Animal Science & Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
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A novel SNP within LIPE gene is highly associated with sheep intramuscular fat content. Small Rumin Res 2022. [DOI: 10.1016/j.smallrumres.2022.106658] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Kumar A, Kaur M, Ahlawat S, Sharma U, Singh MK, Singh KV, Chhabra P, Vijh RK, Yadav A, Arora R. Transcriptomic diversity in longissimus thoracis muscles of Barbari and Changthangi goat breeds of India. Genomics 2021; 113:1639-1646. [PMID: 33862183 DOI: 10.1016/j.ygeno.2021.04.019] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 02/24/2021] [Accepted: 04/07/2021] [Indexed: 01/13/2023]
Abstract
The present study is an attempt to examine the differential expression of genes in longissimus thoracis muscles between meat and wool type Indian goat breeds. Barbari goat is considered the best meat breed while Changthangi is famous for its fine fibre quality. RNA sequencing data was generated from four biological replicates of longissimus thoracis muscles of Barbari and Changthangi goats. A clear demarcation could be observed between the breeds in terms of expression of genes associated with lipid metabolism (FASN, SCD, THRSP, DGAT2 and FABP3). Most significant genes with high connectivity identified by gene co-expression network analysis were associated with triacylglycerol biosynthesis pathway in Barbari goat. Highly interactive genes identified in Changthangi goat were mainly associated with muscle fibre type. This study provides an insight into the differential expression of genes in longissimus thoracis muscles between Barbari and Changthangi goats that are adapted to and reared in different agro-climatic regions.
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Affiliation(s)
- Ashish Kumar
- ICAR-National Bureau of Animal Genetic Resources, Karnal 132001, Haryana, India; Kurukshetra University, Kurukshetra 136119, Haryana, India
| | - Mandeep Kaur
- ICAR-National Bureau of Animal Genetic Resources, Karnal 132001, Haryana, India; Kurukshetra University, Kurukshetra 136119, Haryana, India
| | - Sonika Ahlawat
- ICAR-National Bureau of Animal Genetic Resources, Karnal 132001, Haryana, India.
| | - Upasna Sharma
- ICAR-National Bureau of Animal Genetic Resources, Karnal 132001, Haryana, India
| | - Manoj Kumar Singh
- Incharge Barbari Goat Unit, Genetics and Breeding Division, Central Institute for Research on Goats, Makhdoom, Farah, 281122 Mathura, Uttar Pradesh, India.
| | - Karan Veer Singh
- ICAR-National Bureau of Animal Genetic Resources, Karnal 132001, Haryana, India.
| | - Pooja Chhabra
- ICAR-National Bureau of Animal Genetic Resources, Karnal 132001, Haryana, India
| | - Ramesh Kumar Vijh
- ICAR-National Bureau of Animal Genetic Resources, Karnal 132001, Haryana, India.
| | - Anita Yadav
- Kurukshetra University, Kurukshetra 136119, Haryana, India.
| | - Reena Arora
- ICAR-National Bureau of Animal Genetic Resources, Karnal 132001, Haryana, India.
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Ibrahim AHM. Polymorphisms in hormone-sensitive lipase and leptin receptor genes and their association with growth traits in Barki lambs. Vet World 2021; 14:515-522. [PMID: 33776319 PMCID: PMC7994136 DOI: 10.14202/vetworld.2021.515-522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Accepted: 01/19/2021] [Indexed: 11/16/2022] Open
Abstract
Background and Aim Marker-assisted selection has many advantages over conventional selection in animal breeding. The candidate gene approach has been applied to identify genetic markers associated with economically important traits in livestock. This study was established to investigate variation in the hormone-sensitive lipase (HSL) and leptin receptor (LEPR) genes, and their association with growth traits in Barki lambs. Materials and Methods Records for birth weight (BW), pre-weaning average daily gain (ADG1), weaning weight (WW), post-weaning average daily gain (ADG2), and marketing weight (MW) were obtained from 247 Barki lambs. Polymerase chain reaction-single-stranded conformational polymorphism analyses were used to detect variation in exon 9 of HSL and exon 19 of LEPR. General linear models were used to test for associations between the variation in ovine HSL and LEPR, and growth traits. Results The SSCP banding patterns for HSL showed three variants (H1, H2, and H3), which contained two nucleotide-sequence differences (c.1865C>T and c.2038T>C). Two SSCP banding patterns (L1 and L2) were observed for LEPR and these contained two nucleotide-sequence differences (c.2800G>A and c.2978C>G). The HSL genotype showed no effect on the studied traits. The LEPR genotype was proven to have significant effects (p<0.05) on ADG2 and MW. The presence of the L1 variant was associated (p<0.01) with decreased ADG2 and MW. Conclusion The finding of an association between LEPR gene variation and growth rate after weaning in Barki lambs warrants efforts to improve this trait.
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Affiliation(s)
- Adel H M Ibrahim
- Department of Animal Breeding, Desert Research Center, Cairo, Egypt
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Wang S, Raza SHA, Mei C, Zhu K, Garcia M, Schreurs NM, Liang C, Yang X, Zan L. Transcriptome profiling reveals differential expression of genes potentially involved in muscle and adipose tissue development of cattle. ELECTRON J BIOTECHN 2020. [DOI: 10.1016/j.ejbt.2020.09.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
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Al-Thuwaini TM, Al-Shuhaib MBS, Lepretre F, Mahdi ZA. Co-inherited novel SNPs of the LIPE gene associated with increased carcass dressing and decreased fat-tail weight in Awassi breed. Trop Anim Health Prod 2020; 52:3631-3638. [PMID: 32939705 DOI: 10.1007/s11250-020-02400-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Accepted: 09/11/2020] [Indexed: 12/19/2022]
Abstract
The lipase E hormone-sensitive (LIPE) enzyme is one of the lipolytic enzymes, and it plays a key role in the regulation of adipose tissue deposition. This study was conducted to investigate the possible association between the LIPE gene variations and the main body weight measurements in Awassi sheep. A total of 160 of sexually mature Awassi rams (Ovis aries) that aged between 2 and 3 years were included in the present study. Genomic DNA was extracted and two specific PCR amplicons were designed to amplify two coding regions within the LIPE gene. Genotyping experiments were performed using polymerase chain reaction-single-strand conformational polymorphism (PCR-SSCP). Two different SSCP banding patterns were identified, CC and CD in exon 2, and AA and AT in exon 9. Five novel single-nucleotide polymorphisms (SNPs) were detected by sequencing, namely g.151C > A and g.198C > T in exon 2, and g.213G > C, g.226G > T, and g.232A > C in exon 9. Haplotype block analysis showed strong linkage disequilibrium values between the two SNPs in exon 2 and the three SNPs in exon 9. Association analysis of haplotypes with carcass traits demonstrated a significantly higher dressing percentage (P < 0.05) and lower fat tail weight (FTW) in CACT and GCGTAC haplotypes made these haplotypes more favorable for human consumption. The current research is the first one to report a tight association between the LIPE genetic polymorphism and the dressing percentage and FTW traits, suggesting a pivotal role played by these co-inherited SNPs in the metabolism of carcass traits in sheep.
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Affiliation(s)
- Tahreer M Al-Thuwaini
- Department of Animal Production, College of Agriculture, Al-Qasim Green University, Al-Qasim, Babil, 51001, Iraq.
| | - Mohammed Baqur S Al-Shuhaib
- Department of Animal Production, College of Agriculture, Al-Qasim Green University, Al-Qasim, Babil, 51001, Iraq
| | - Frederic Lepretre
- Plateau de genomique fonctionnelle et structurale, CHU Lille, University of Lille, Lille, France
| | - Zainab A Mahdi
- Department of Animal Production, College of Agriculture, Al-Qasim Green University, Al-Qasim, Babil, 51001, Iraq
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Gui LS, Raza SHA, Memon S, Li Z, Abd El-Aziz AH, Ullah I, Jahejo AR, Shoorei H, Khan R, Quan G, Liu GY. Association of hormone-sensitive lipase (HSL) gene polymorphisms with the intramuscular fat content in two Chinese beef cattle breeds. Genomics 2020; 112:3883-3889. [PMID: 32619575 DOI: 10.1016/j.ygeno.2020.06.037] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 06/06/2020] [Accepted: 06/22/2020] [Indexed: 11/28/2022]
Abstract
Hormone-sensitive lipase (HSL) was considered as an essential enzyme in glucolipid metabolism. It has been proposed to be a lead candidate gene for genetic markers of lipid deposition in livestock. The aim of this study was to identify sequence variants (SVs) of the bovine HSL gene and evaluate the relations to intramuscular fat in two indigenous Chinese beef cattle breeds. Expression analysis by quantitative real-time polymerase chain reactions (qPCR) indicated that expression levels of bovine HSL gene were highest in the perirenal fat and heart within two different age stage (adult and calf), respectively. Five SVs were identified by direct DNA sequencing, which included four missense mutations (g.16563C>T, g.16734G>A, g.16896A>G, g.17388G>T) in exon 8 and a synonymous mutation (g.17402C>T) in exon 9. Population genetic analysis showed that except for g.16563C>T and g.17402C>T, all the other detected SVs strongly affected the bovine intramuscular fat content (P < 0.01 or P < 0.05). The individuals with Hap5/5 diplotypes (CC-GG-GG-GG-CC) was highly significantly associated with intramuscular fat content than the other diplotypes (P < 0.01). The above results suggested that the HSL gene can used as potential candidate markers gene for the beef breed improvement through marker assisted selection in Chinese cattle breeds.
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Affiliation(s)
- Lin-Sheng Gui
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, Qinghai Province 810016, People's Republic of China
| | - Sayed Haidar Abbas Raza
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, People's Republic of China.
| | - Sameeullah Memon
- Yunnan Animal Science and Veterinary Institute, Kunming 650224, People's Republic of China
| | - Zhou Li
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, Qinghai Province 810016, People's Republic of China
| | - Ayman Hassan Abd El-Aziz
- Animal Husbandry and Animal Wealth Development Department, Faculty of Veterinary Medicine, Damanhour University, Damanhour 22511, Egypt
| | - Irfan Ullah
- Department of Biological Science, Karakoram International University, Ghizer Campus, Gilgit, Baltistan 15200, Pakistan
| | - Ali Raza Jahejo
- College of Animal Science and Veterinary Medicine, Shanxi Agricultural University, Taigu 030801, China
| | - Hamed Shoorei
- Department of Anatomical Sciences, Faculty of Medicine, Birjand University of Medical Sciences, Birjand, Iran
| | - Rajwali Khan
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, People's Republic of China
| | - Guobo Quan
- Yunnan Animal Science and Veterinary Institute, Kunming 650224, People's Republic of China.
| | - Gui Yao Liu
- Poyang Lake Eco-economy Research Center, Jiujiang University, Jiujiang, Jiangxi Province 332005, People's Republic of China.
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Comparative genome-wide methylation analysis of longissimus dorsi muscles between Japanese black (Wagyu) and Chinese Red Steppes cattle. PLoS One 2017; 12:e0182492. [PMID: 28771560 PMCID: PMC5542662 DOI: 10.1371/journal.pone.0182492] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Accepted: 07/07/2017] [Indexed: 12/02/2022] Open
Abstract
DNA methylation is an important epigenetic mechanism involved in expression of genes in many biological processes including muscle growth and development. Its effects on economically important traits are evinced from reported significant differences in meat quality traits between Japanese black (Wagyu) and Chinese Red Steppes cattle, thus presenting a unique model for analyzing the effects of DNA methylation on these traits. In the present study, we performed whole genome DNA methylation analysis in the two breeds by whole genome bisulfite sequencing (WGBS). Overall, 23150 differentially methylated regions (DMRs) were identified which were located in 8596 genes enriched in 9922 GO terms, of which 1046 GO terms were significantly enriched (p<0.05) including lipid translocation (GO: 0034204) and lipid transport (GO: 0015914). KEGG analysis showed that the DMR related genes were distributed among 276 pathways. Correlation analysis found that 331 DMRs were negatively correlated with the expression levels of differentially expressed genes (DEGs) with 21 DMRs located in promoter regions. Our results identified novel candidate DMRs and DEGs correlated with meat quality traits, which will be valuable for future genomic and epigenomic studies of muscle development and for marker assisted selection of meat quality traits.
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Goszczynski DE, Papaleo-Mazzucco J, Ripoli MV, Villarreal EL, Rogberg-Muñoz A, Mezzadra CA, Melucci LM, Giovambattista G. Genetic Variation in FABP4 and Evaluation of Its Effects on Beef Cattle Fat Content. Anim Biotechnol 2017; 28:211-219. [DOI: 10.1080/10495398.2016.1262868] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Daniel E. Goszczynski
- IGEVET – Instituto de Genética Veterinaria “Ing. Fernando Noel Dulout” (UNLP-CONICET LA PLATA), Facultad de Ciencias Veterinarias UNLP, La Plata, Argentina
| | - Juliana Papaleo-Mazzucco
- Unidad Integrada INTA Balcarce, Facultad de Ciencias Agrarias, Universidad Nacional de Mar del Plata (UNMdP), Balcarce, Argentina
| | - María V. Ripoli
- IGEVET – Instituto de Genética Veterinaria “Ing. Fernando Noel Dulout” (UNLP-CONICET LA PLATA), Facultad de Ciencias Veterinarias UNLP, La Plata, Argentina
| | - Edgardo L. Villarreal
- Unidad Integrada INTA Balcarce, Facultad de Ciencias Agrarias, Universidad Nacional de Mar del Plata (UNMdP), Balcarce, Argentina
| | - Andrés Rogberg-Muñoz
- IGEVET – Instituto de Genética Veterinaria “Ing. Fernando Noel Dulout” (UNLP-CONICET LA PLATA), Facultad de Ciencias Veterinarias UNLP, La Plata, Argentina
| | - Carlos A. Mezzadra
- Unidad Integrada INTA Balcarce, Facultad de Ciencias Agrarias, Universidad Nacional de Mar del Plata (UNMdP), Balcarce, Argentina
| | - Lilia M. Melucci
- Unidad Integrada INTA Balcarce, Facultad de Ciencias Agrarias, Universidad Nacional de Mar del Plata (UNMdP), Balcarce, Argentina
| | - Guillermo Giovambattista
- IGEVET – Instituto de Genética Veterinaria “Ing. Fernando Noel Dulout” (UNLP-CONICET LA PLATA), Facultad de Ciencias Veterinarias UNLP, La Plata, Argentina
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Growth, carcass and meat quality traits in beef from Angus, Hereford and cross-breed grazing steers, and their association with SNPs in genes related to fat deposition metabolism. Meat Sci 2016; 114:121-129. [DOI: 10.1016/j.meatsci.2015.12.018] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2015] [Revised: 12/11/2015] [Accepted: 12/23/2015] [Indexed: 11/18/2022]
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Goszczynski DE, Mazzucco JP, Ripoli MV, Villarreal EL, Rogberg-Muñoz A, Mezzadra CA, Melucci LM, Giovambattista G. Genetic characterisation of PPARG, CEBPA and RXRA, and their influence on meat quality traits in cattle. JOURNAL OF ANIMAL SCIENCE AND TECHNOLOGY 2016; 58:14. [PMID: 27042330 PMCID: PMC4818460 DOI: 10.1186/s40781-016-0095-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/17/2015] [Accepted: 03/15/2016] [Indexed: 11/14/2022]
Abstract
Background Peroxisome proliferator-activated receptor gamma (PPARG), CCAAT/enhancer binding protein alpha (CEBPA) and retinoid X receptor alpha (RXRA) are nuclear transcription factors that play important roles in regulation of adipogenesis and fat deposition. The objectives of this study were to characterise the variability of these three candidate genes in a mixed sample panel composed of several cattle breeds with different meat quality, validate single nucleotide polymorphisms (SNPs) in a local crossbred population (Angus - Hereford - Limousin) and evaluate their effects on meat quality traits (backfat thickness, intramuscular fat content and fatty acid composition), supporting the association tests with bioinformatic predictive studies. Results Globally, nine SNPs were detected in the PPARG and CEBPA genes within our mixed panel, including a novel SNP in the latter. Three of these nine, along with seven other SNPs selected from the Single Nucleotide Polymorphism database (SNPdb), including SNPs in the RXRA gene, were validated in the crossbred population (N = 260). After validation, five of these SNPs were evaluated for genotype effects on fatty acid content and composition. Significant effects were observed on backfat thickness and different fatty acid contents (P < 0.05). Some of these SNPs caused slight differences in mRNA structure stability and/or putative binding sites for proteins. Conclusions PPARG and CEBPA showed low to moderate variability in our sample panel. Variations in these genes, along with RXRA, may explain part of the genetic variation in fat content and composition. Our results may contribute to knowledge about genetic variation in meat quality traits in cattle and should be evaluated in larger independent populations. Electronic supplementary material The online version of this article (doi:10.1186/s40781-016-0095-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Daniel Estanislao Goszczynski
- Instituto de Genética Veterinaria "Ing. Fernando Noel Dulout" (IGEVET), CONICET, Facultad de Ciencias Veterinarias, Universidad Nacional de La Plata, CC 296, La Plata, B1900AVW Argentina ; Fellow of the Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Juliana Papaleo Mazzucco
- Unidad Integrada INTA Balcarce-Facultad de Ciencias Agrarias, Universidad Nacional de Mar del Plata, Balcarce, Argentina
| | - María Verónica Ripoli
- Instituto de Genética Veterinaria "Ing. Fernando Noel Dulout" (IGEVET), CONICET, Facultad de Ciencias Veterinarias, Universidad Nacional de La Plata, CC 296, La Plata, B1900AVW Argentina
| | - Edgardo Leopoldo Villarreal
- Unidad Integrada INTA Balcarce-Facultad de Ciencias Agrarias, Universidad Nacional de Mar del Plata, Balcarce, Argentina
| | - Andrés Rogberg-Muñoz
- Instituto de Genética Veterinaria "Ing. Fernando Noel Dulout" (IGEVET), CONICET, Facultad de Ciencias Veterinarias, Universidad Nacional de La Plata, CC 296, La Plata, B1900AVW Argentina
| | - Carlos Alberto Mezzadra
- Unidad Integrada INTA Balcarce-Facultad de Ciencias Agrarias, Universidad Nacional de Mar del Plata, Balcarce, Argentina
| | - Lilia Magdalena Melucci
- Unidad Integrada INTA Balcarce-Facultad de Ciencias Agrarias, Universidad Nacional de Mar del Plata, Balcarce, Argentina
| | - Guillermo Giovambattista
- Instituto de Genética Veterinaria "Ing. Fernando Noel Dulout" (IGEVET), CONICET, Facultad de Ciencias Veterinarias, Universidad Nacional de La Plata, CC 296, La Plata, B1900AVW Argentina
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