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Bejarano DH, Martínez RA, Rocha JF. Genome-wide association study for growth traits in Blanco Orejinegro and Romosinuano cattle. Trop Anim Health Prod 2023; 55:358. [PMID: 37848724 PMCID: PMC10581918 DOI: 10.1007/s11250-023-03743-9] [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: 12/21/2022] [Accepted: 09/12/2023] [Indexed: 10/19/2023]
Abstract
Growth traits are economically important characteristics for the genetic improvement of local cattle breeds. Genome-wide association studies (GWAS) provide valuable information to enhance the understanding on the genetics of complex traits. The aim of this study was to perform a GWAS to identify genomic regions and genes associated to birth weight, weaning weight adjusted for 240 days, 16 months, and 24 months weight in Romosinuano (ROMO) and Blanco Orejinegro (BON) cattle. A single-step genomic-BLUP was implemented using 596 BON and 569 ROMO individuals that were genotyped with an Illumina BovineSNP50 BeadChip. There were 25 regions of interest identified on different chromosomes, with few of them simultaneously associated with two or more growth traits and some were common to both breeds. The gene mapping allowed to find 173 annotations on these regions, from which 49 represent potential candidate genes with known growth-related functions in cattle and other species. Among the regions that were associated with several growth traits, that at 24 - 27 MB of BTA14, has important candidate genes such as LYPLA1, XKR4, TMEM68 and PLAG1. Another region of interest at 0.40-0.77 Mb of BTA23 was identified in both breeds, containing KHDRBS2 as a potential candidate gene influencing body weight. Future studies targeting these regions could provide more knowledge to uncover the genetic architecture underlying growth traits in BON and ROMO cattle. The genomic regions and genes identified in this study could be used to improve the prediction of genetic merit for growth traits in these creole cattle breeds.
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Affiliation(s)
- Diego H Bejarano
- Corporación Colombiana de Investigación Agropecuaria -AGROSAVIA. Centro de Investigación Tibaitatá, Km. 14, Mosquera, Cundinamarca, Colombia
| | - Rodrigo A Martínez
- Corporación Colombiana de Investigación Agropecuaria -AGROSAVIA. Centro de Investigación Tibaitatá, Km. 14, Mosquera, Cundinamarca, Colombia
| | - Juan F Rocha
- Corporación Colombiana de Investigación Agropecuaria -AGROSAVIA. Centro de Investigación Tibaitatá, Km. 14, Mosquera, Cundinamarca, Colombia.
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2
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Sun T, Pei S, Liu Y, Hanif Q, Xu H, Chen N, Lei C, Yue X. Whole genome sequencing of simmental cattle for SNP and CNV discovery. BMC Genomics 2023; 24:179. [PMID: 37020271 PMCID: PMC10077681 DOI: 10.1186/s12864-023-09248-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Accepted: 03/14/2023] [Indexed: 04/07/2023] Open
Abstract
BACKGROUD The single nucleotide polymorphisms (SNPs) and copy number variations (CNVs) are two major genomic variants, which play crucial roles in evolutionary and phenotypic diversity. RESULTS In this study, we performed a comprehensive analysis to explore the genetic variations (SNPs and CNVs) of high sperm motility (HSM) and poor sperm motility (PSM) Simmental bulls using the high-coverage (25×) short-read next generation sequencing and single-molecule long reads sequencing data. A total of ~ 15 million SNPs and 2,944 CNV regions (CNVRs) were detected in Simmental bulls, and a set of positive selected genes (PSGs) and CNVRs were found to be overlapped with quantitative trait loci (QTLs) involving immunity, muscle development, reproduction, etc. In addition, we detected two new variants in LEPR, which may be related to the artificial breeding to improve important economic traits. Moreover, a set of genes and pathways functionally related to male fertility were identified. Remarkably, a CNV on SPAG16 (chr2:101,427,468 - 101,429,883) was completely deleted in all poor sperm motility (PSM) bulls and half of the bulls in high sperm motility (HSM), which may play a crucial role in the bull-fertility. CONCLUSIONS In conclusion, this study provides a valuable genetic variation resource for the cattle breeding and selection programs.
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Affiliation(s)
- Ting Sun
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Engineering Research Center of Grassland Industry, College of Pastoral Agriculture Science and Technology, Ministry of Education, Lanzhou University, Lanzhou, 730020, P. R. China
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, Shaanxi, China
- College of Life Sciences, Shaanxi Normal University, Xi'an, 710062, China
| | - Shengwei Pei
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Engineering Research Center of Grassland Industry, College of Pastoral Agriculture Science and Technology, Ministry of Education, Lanzhou University, Lanzhou, 730020, P. R. China
| | - Yangkai Liu
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Engineering Research Center of Grassland Industry, College of Pastoral Agriculture Science and Technology, Ministry of Education, Lanzhou University, Lanzhou, 730020, P. R. China
| | - Quratulain Hanif
- Computational Biology Laboratory, Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering, Faisalabad, Pakistan
- Department of Biotechnology, Pakistan Institute of Engineering and Applied Sciences, Nilore, Islamabad, Pakistan
| | - Haiyue Xu
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Engineering Research Center of Grassland Industry, College of Pastoral Agriculture Science and Technology, Ministry of Education, Lanzhou University, Lanzhou, 730020, P. R. China
| | - Ningbo Chen
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Chuzhao Lei
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Xiangpeng Yue
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Engineering Research Center of Grassland Industry, College of Pastoral Agriculture Science and Technology, Ministry of Education, Lanzhou University, Lanzhou, 730020, P. R. China.
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3
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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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4
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Zheng XD, Cheng J, Qin WJ, Balsai N, Shang XJ, Zhang MT, Chen HQ. Whole Transcriptome Analysis Identifies the Taxonomic Status of a New Chinese Native Cattle Breed and Reveals Genes Related to Body Size. Front Genet 2020; 11:562855. [PMID: 33240316 PMCID: PMC7670488 DOI: 10.3389/fgene.2020.562855] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2020] [Accepted: 09/11/2020] [Indexed: 11/15/2022] Open
Abstract
Wandong (WD) cattle has recently been identified as a new Chinese native cattle breed by the National Commission for Livestock and Poultry Genetic Resources. The population size of this breed is less than 10,000. WD cattle and Dabieshan (DB) cattle are sympatric but are raised in different ecological environments, on mountains and plains, respectively, and the body sizes of these two breeds are markedly different. Blood samples were obtained from 8 adult female WD cattle and 7 adult female DB cattle (24 months old). The total RNA was extracted from leukocyte cells, and sequencing experiments were conducted on the Illumina HiSeqTM 4000 platform. After the removal of one outlier sample from the WD cattle breed as determined by principal component analysis (PCA), phylogenetic and population structure analyses indicated that WD and DB cattle formed a distinct Central China cattle group and showed evidence of hybridization between Bos. taurus and Bos. indicus. The immune-regulator CD48 (P = 1.3E-6) was associated with breed-specific traits according to loss-of-function variant enrichment analysis. In addition, 113 differentially expressed genes were identified between the two breeds, many of which are associated with the regulation of body growth, which is the major difference between the two breeds. This study showed that WD cattle belong to the group of hybrids between Bos. Taurus and Bos. indicus, and one novel gene associated with breed traits and multiple differentially expressed genes between these two closely related breeds was identified. The results provide insights into the genetic mechanisms that underlie economically important traits, such as body size, in cattle.
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Affiliation(s)
- Xiao-Dong Zheng
- School of Animal Science and Technology, Anhui Agricultural University, Hefei, China.,Key Laboratory of Anhui Local Livestock and Poultry Genetic Resources Conservation and Biobreeding, Hefei, China.,Department of Dermatology, The First Affiliated Hospital of Anhui Medical University, Hefei, China.,Key Laboratory of Dermatology (Anhui Medical University), Ministry of Education, Hefei, China.,Key Laboratory of Major Autoimmune Diseases, Hefei, China
| | - Jin Cheng
- School of Animal Science and Technology, Anhui Agricultural University, Hefei, China.,Key Laboratory of Anhui Local Livestock and Poultry Genetic Resources Conservation and Biobreeding, Hefei, China
| | - Wen-Juan Qin
- School of Animal Science and Technology, Anhui Agricultural University, Hefei, China.,Key Laboratory of Anhui Local Livestock and Poultry Genetic Resources Conservation and Biobreeding, Hefei, China.,International Immunization Center, Anhui Agricultural University, Hefei, China
| | - Nyamsuren Balsai
- School of Animal Science and Technology, Anhui Agricultural University, Hefei, China.,Key Laboratory of Anhui Local Livestock and Poultry Genetic Resources Conservation and Biobreeding, Hefei, China
| | - Xuan-Jian Shang
- School of Animal Science and Technology, Anhui Agricultural University, Hefei, China.,Key Laboratory of Anhui Local Livestock and Poultry Genetic Resources Conservation and Biobreeding, Hefei, China
| | - Meng-Ting Zhang
- School of Animal Science and Technology, Anhui Agricultural University, Hefei, China.,Key Laboratory of Anhui Local Livestock and Poultry Genetic Resources Conservation and Biobreeding, Hefei, China
| | - Hong-Quan Chen
- School of Animal Science and Technology, Anhui Agricultural University, Hefei, China.,Key Laboratory of Anhui Local Livestock and Poultry Genetic Resources Conservation and Biobreeding, Hefei, China.,International Immunization Center, Anhui Agricultural University, Hefei, China
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5
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Ghoneim M, Ogaly H, Gouda E, El-Behairy A. Prediction of desirable genotype patterns in Baladi beef cattle and water buffalo by identification of new leptin gene SNPs. Livest Sci 2016. [DOI: 10.1016/j.livsci.2015.09.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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6
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Jonas E, Martin G, Celi P, Li L, Soattin M, Thomson P, Raadsma H. Association of polymorphisms in leptin and leptin receptor genes with circulating leptin concentrations, production and efficiency traits in sheep. Small Rumin Res 2016. [DOI: 10.1016/j.smallrumres.2016.01.010] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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7
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Shi T, Xu Y, Yang M, Huang Y, Lan X, Lei C, Qi X, Yang X, Chen H. Copy number variations atLEPRgene locus associated with gene expression and phenotypic traits in Chinese cattle. Anim Sci J 2015; 87:336-43. [DOI: 10.1111/asj.12531] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2015] [Revised: 07/11/2015] [Accepted: 07/29/2015] [Indexed: 11/30/2022]
Affiliation(s)
- Tao Shi
- College of Animal Science and Technology, Shaanxi Key Laboratory of Molecular Biology for Agriculture; Northwest A&F University; Yangling China
| | - Yao Xu
- College of Animal Science and Technology, Shaanxi Key Laboratory of Molecular Biology for Agriculture; Northwest A&F University; Yangling China
| | - Mingjuan Yang
- College of Animal Science and Technology, Shaanxi Key Laboratory of Molecular Biology for Agriculture; Northwest A&F University; Yangling China
| | - Yongzhen Huang
- College of Animal Science and Technology, Shaanxi Key Laboratory of Molecular Biology for Agriculture; Northwest A&F University; Yangling China
| | - Xianyong Lan
- College of Animal Science and Technology, Shaanxi Key Laboratory of Molecular Biology for Agriculture; Northwest A&F University; Yangling China
| | - Chuzhao Lei
- College of Animal Science and Technology, Shaanxi Key Laboratory of Molecular Biology for Agriculture; Northwest A&F University; Yangling China
| | - Xinglei Qi
- Biyang Bureau of Animal Husbandry of Biyang County; Biyang Henan China
| | - Xiaoming Yang
- Institute of Animal Husbandry and Veterinary; Shanxi Academy of Agricultural Sciences; Taiyuan Shanxi China
| | - Hong Chen
- College of Animal Science and Technology, Shaanxi Key Laboratory of Molecular Biology for Agriculture; Northwest A&F University; Yangling China
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8
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Gutiérrez-Gil B, Arranz JJ, Wiener P. An interpretive review of selective sweep studies in Bos taurus cattle populations: identification of unique and shared selection signals across breeds. Front Genet 2015; 6:167. [PMID: 26029239 PMCID: PMC4429627 DOI: 10.3389/fgene.2015.00167] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2014] [Accepted: 04/13/2015] [Indexed: 12/11/2022] Open
Abstract
This review compiles the results of 21 genomic studies of European Bos taurus breeds and thus provides a general picture of the selection signatures in taurine cattle identified by genome-wide selection-mapping scans. By performing a comprehensive summary of the results reported in the literature, we compiled a list of 1049 selection sweeps described across 37 cattle breeds (17 beef breeds, 14 dairy breeds, and 6 dual-purpose breeds), and four different beef-vs.-dairy comparisons, which we subsequently grouped into core selective sweep (CSS) regions, defined as consecutive signals within 1 Mb of each other. We defined a total of 409 CSSs across the 29 bovine autosomes, 232 (57%) of which were associated with a single-breed (Single-breed CSSs), 134 CSSs (33%) were associated with a limited number of breeds (Two-to-Four-breed CSSs) and 39 CSSs (9%) were associated with five or more breeds (Multi-breed CSSs). For each CSS, we performed a candidate gene survey that identified 291 genes within the CSS intervals (from the total list of 5183 BioMart-extracted genes) linked to dairy and meat production, stature, and coat color traits. A complementary functional enrichment analysis of the CSS positional candidates highlighted other genes related to pathways underlying behavior, immune response, and reproductive traits. The Single-breed CSSs revealed an over-representation of genes related to dairy and beef production, this was further supported by over-representation of production-related pathway terms in these regions based on a functional enrichment analysis. Overall, this review provides a comparative map of the selection sweeps reported in European cattle breeds and presents for the first time a characterization of the selection sweeps that are found in individual breeds. Based on their uniqueness, these breed-specific signals could be considered as “divergence signals,” which may be useful in characterizing and protecting livestock genetic diversity.
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Affiliation(s)
| | - Juan J Arranz
- Departamento de Producción Animal, Universidad de León León, Spain
| | - Pamela Wiener
- Division of Genetics and Genomics, Roslin Institute and R(D)SVS, University of Edinburgh Midlothian, UK
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9
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De Matteis G, Scatà MC, Catillo G, Terzano GM, Grandoni F, Napolitano F. Characterization of leptin receptor gene in Bubalus bubalis and association analysis with body measurement traits. Mol Biol Rep 2014; 42:1049-57. [DOI: 10.1007/s11033-014-3844-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2013] [Accepted: 11/22/2014] [Indexed: 11/29/2022]
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10
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Somavilla AL, Sonstegard TS, Higa RH, Rosa AN, Siqueira F, Silva LOC, Torres Júnior RAA, Coutinho LL, Mudadu MA, Alencar MM, Regitano LCA. A genome-wide scan for selection signatures in Nellore cattle. Anim Genet 2014; 45:771-81. [DOI: 10.1111/age.12210] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/15/2014] [Indexed: 11/27/2022]
Affiliation(s)
- A. L. Somavilla
- Programa de Pós-Graduação em Genética e Melhoramento Animal; UNESP/FCAV; Jaboticabal Brasil
| | - T. S. Sonstegard
- Bovine Functional Genomics Laboratory; ANRI; USDA-ARS; Beltsville MD USA
| | - R. H. Higa
- Embrapa Informática Agropecuária; Campinas Brasil
| | - A. N. Rosa
- Embrapa Gado de Corte; Campo Grande Brasil
| | | | | | | | - L. L. Coutinho
- Escola Superior de Agricultura Luiz de Queiroz (Esalq); USP; Piracicaba Brasil
- CNPq Fellow; Brasília Distrito Federal Brasil
| | | | - M. M. Alencar
- Embrapa Pecuária Sudeste; São Carlos Brasil
- CNPq Fellow; Brasília Distrito Federal Brasil
| | - L. C. A. Regitano
- Embrapa Pecuária Sudeste; São Carlos Brasil
- CNPq Fellow; Brasília Distrito Federal Brasil
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11
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Huang H, Wei Y, Meng Z, Zhang Y, Liu X, Guo L, Luo J, Chen G, Lin H. Polymorphisms of leptin-b gene associated with growth traits in orange-spotted grouper (Epinephelus coioides). Int J Mol Sci 2014; 15:11996-2006. [PMID: 25003640 PMCID: PMC4139826 DOI: 10.3390/ijms150711996] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2014] [Revised: 05/26/2014] [Accepted: 06/06/2014] [Indexed: 12/01/2022] Open
Abstract
In mammals, leptin has been demonstrated to perform important roles in many physiological activities and to influence development, growth, metabolism and reproduction. However, in fish, its function is still unclear. Duplicate leptin genes, leptin-a and leptin-b, have been identified in the orange-spotted grouper. In the present study, the polymorphisms in the leptin-b gene of the orange-spotted grouper were detected, and the relation between these polymorphisms and 12 growth traits were analyzed. Six polymorphisms (including 3 single nucleotide polymorphisms (c.14G>A, c.93A>G, c.149G>A) in exon 1, 2 SNPs (c.181A>G, c.193G>A) in intron 1, and 1 SNP (c.360C>T) in exon 2) were identified and genotyped from 200 different individuals. The results revealed that the SNP c.149G>A was significantly associated with growth traits, that the heterozygous mutation genotype GA having negative effects on growth traits. However, the other five SNPs (c.14G>A, c.93A>G, c.181A>G, c.193G>A, c.360C>T) did not show significant associations with all the growth traits. Compared with our findings in leptin-a gene, the results suggested that the leptin-a hormone has more important physiological effects in fish bodies than the leptin-b type. Moreover, leptin genes were supposed to be one class of major candidate genes of regulating growth traits in the orange-spotted grouper.
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Affiliation(s)
- Hai Huang
- Sanya Science & Technology Academy of Hainan National Breeding and Multiplication, Sanya 572000, China.
| | - Yun Wei
- Key Laboratory of Tropical Biology Resources, Ministry of Education, College of Ocean, Hainan University, Haikou 570228, China.
| | - Zining Meng
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, College of Life Sciences, Sun Yat-Sen (Zhongshan) University, Guangzhou 510275, China.
| | - Yong Zhang
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, College of Life Sciences, Sun Yat-Sen (Zhongshan) University, Guangzhou 510275, China.
| | - Xiaochun Liu
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, College of Life Sciences, Sun Yat-Sen (Zhongshan) University, Guangzhou 510275, China.
| | - Liang Guo
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, College of Life Sciences, Sun Yat-Sen (Zhongshan) University, Guangzhou 510275, China.
| | - Jian Luo
- Key Laboratory of Tropical Biology Resources, Ministry of Education, College of Ocean, Hainan University, Haikou 570228, China.
| | - Guohua Chen
- Key Laboratory of Tropical Biology Resources, Ministry of Education, College of Ocean, Hainan University, Haikou 570228, China.
| | - Haoran Lin
- Key Laboratory of Tropical Biology Resources, Ministry of Education, College of Ocean, Hainan University, Haikou 570228, China.
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Haldar A, French MC, Brauning R, Edwards SJ, O'Connell AR, Farquhar PA, Davis GH, Johnstone PD, Juengel JL. Single-Nucleotide Polymorphisms in the LEPR Gene Are Associated with Divergent Phenotypes for Age at Onset of Puberty in Davisdale Ewes1. Biol Reprod 2014; 90:33. [PMID: 24389871 DOI: 10.1095/biolreprod.113.115923] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Affiliation(s)
- Avijit Haldar
- Animal Reproduction Division, Indian Council of Agriculture Research Complex for North Eastern Hill Region, Tripura Centre, Lembucherra, West Tripura, India
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13
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Heifer fertility and carry over consequences for life time production in dairy and beef cattle. Animal 2014; 8 Suppl 1:91-104. [DOI: 10.1017/s1751731114000755] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
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14
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Lai X, Zhang C, Wang J, Wang C, Lan X, Zhang C, Lei C, Chen H. mRNA expression pattern and association study with growth traits of bovine vaspin gene. Mol Biol Rep 2013; 40:4499-505. [PMID: 23657594 DOI: 10.1007/s11033-013-2542-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2012] [Accepted: 04/29/2013] [Indexed: 02/01/2023]
Abstract
Visceral adipose tissue-derived serine protease inhibitor (vaspin) is an interesting novel adipocytokine with insulin-sensitizing effects. Some studies have suggested that vaspin could play an important role in the development of obesity and metabolic disorders. However, the tissue expression patterns in cattle and impact of vaspin gene variants on the growth traits has not been determined yet. Herein, we firstly investigated the tissue expression patterns of vaspin gene in new born and adult cattle. The results showed that vaspin was ubiquitously expressed in most tissues and strongly expressed in the heart, skeletal muscle and fat. Then, genetic variants within bovine vaspin gene were screened in 1235 individuals from five Chinese indigenous cattle breeds. Two novel mutations in coding region (NW_001494061: g.1124477 G>A and g.1118561 T>C) of bovine vaspin gene were identified using MspI PCR-RFLP and HhaI ACRS PCR-RFLP detection. Association analysis revealed both two mutations were significantly associated with bodyweight and chest girth at 24 months in cattle (P < 0.05). Therefore, the MspI and HhaI genetic variants of bovine vaspin gene were recommended as DNA markers related to growth traits through marker-assisted selection for genetics and breeding in cattle.
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Affiliation(s)
- Xinsheng Lai
- College of Animal Science and Technology, Northwest A&F University, No. 22 Xinong Road, Yangling, Shaanxi, 712100, People's Republic of China.
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15
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Wei Y, Huang H, Meng Z, Zhang Y, Luo J, Chen G, Lin H. Single nucleotide polymorphisms in the leptin-a gene and associations with growth traits in the orange-spotted grouper (Epinephelus coioides). Int J Mol Sci 2013; 14:8625-37. [PMID: 23609495 PMCID: PMC3645766 DOI: 10.3390/ijms14048625] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2013] [Revised: 04/11/2013] [Accepted: 04/16/2013] [Indexed: 12/26/2022] Open
Abstract
Leptin is a multifunctional protein involved in processes such as body weight regulation, energy expenditure, fat metabolism, food intake, and appetite regulation. Duplicate leptin genes, leptin-a and leptin-b, were previously detected in the orange-spotted grouper. In this study, we cloned the full-length open reading frame (ORF) of the leptin-a gene in the orange-spotted grouper, searched for polymorphisms, and performed association analyses between these polymorphisms and seven growth traits. Six polymorphisms, consisting of 2 SNPs in intron 1 (c.182T > G, c.183G > T) and 4 SNPs in exon 2 (c.339C > G, c.345C > T, c.447G > A, c.531C > T), were identified and genotyped in 200 individuals. The c.182T > G and c.183G > T polymorphisms showed complete linkage and were analyzed together. Association analyses revealed that the c.182 + 183TG > GT polymorphism was significantly associated with body weight (BWT) and body width (BWH), with the AB (TG/GT) genotype showing positive effects on growth traits. Additionally, the SNP c.447G > A was significantly associated with BWT, BWH, overall length (OL), trunk width (TW), and head length (HL), with the GA genotype displaying positive effects on growth traits. The c.531C > T SNP showed a close association between the TT genotype and decreased growth. Our results demonstrate that several polymorphisms in the leptin-a gene are associated with growth traits and can be used for marker-assisted selection (MAS) in orange-spotted grouper populations.
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Affiliation(s)
- Yun Wei
- Key Laboratory of Tropical Biology Resources, Ministry of Education, College of Ocean, Hainan University, Haikou 570228, China; E-Mails: (Y.W.); (J.L.); (G.C.)
- Sanya Science & Technology Academy of Hainan National Breeding and Multiplication, Sanya 572000, China
| | - Hai Huang
- Sanya Science & Technology Academy of Hainan National Breeding and Multiplication, Sanya 572000, China
| | - Zining Meng
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, College of Life Sciences, Sun Yat-Sen (Zhongshan) University, Guangzhou 510275, China; E-Mails: (Z.M.); (Y.Z.)
| | - Yong Zhang
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, College of Life Sciences, Sun Yat-Sen (Zhongshan) University, Guangzhou 510275, China; E-Mails: (Z.M.); (Y.Z.)
| | - Jian Luo
- Key Laboratory of Tropical Biology Resources, Ministry of Education, College of Ocean, Hainan University, Haikou 570228, China; E-Mails: (Y.W.); (J.L.); (G.C.)
| | - Guohua Chen
- Key Laboratory of Tropical Biology Resources, Ministry of Education, College of Ocean, Hainan University, Haikou 570228, China; E-Mails: (Y.W.); (J.L.); (G.C.)
| | - Haoran Lin
- Key Laboratory of Tropical Biology Resources, Ministry of Education, College of Ocean, Hainan University, Haikou 570228, China; E-Mails: (Y.W.); (J.L.); (G.C.)
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, College of Life Sciences, Sun Yat-Sen (Zhongshan) University, Guangzhou 510275, China; E-Mails: (Z.M.); (Y.Z.)
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Abstract
Fat affects meat quality, value and production efficiency as well as providing energy reserves for pregnancy and lactation in farm livestock. Leptin, the adipocyte product of the obese (ob) gene, was quickly seen as a predictor of body fat content in animals approaching slaughter and an aid to assessing reproductive readiness in females. Its participation in inflammation and immune responses that help animals survive infection and trauma has clear additional relevance to meat and milk production. Furthermore, almost a decade of discoveries of nucleotide polymorphisms in the leptin and leptin receptor genes has suggested useful applications relating to feed intake regulation, the efficiency of feed use, the composition of growth, the timing of puberty, mammogenesis and mammary gland function and fertility in cattle, pigs and poultry. The current review attempts to summarise where research has taken us in each of these aspects and speculates on where future research might lead.
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Reicher S, Ramos-Nieves JM, Hileman SM, Boisclair YR, Gootwine E, Gertler A. Nonsynonymous natural genetic polymorphisms in the bovine leptin gene affect biochemical and biological characteristics of the mature hormone. J Anim Sci 2011; 90:410-8. [PMID: 21926317 DOI: 10.2527/jas.2011-4378] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Leptin (LEP) is a cytokine-like hormone proven to be involved in diverse biological processes. In livestock, it regulates feed intake, BW homeostasis, and energy balance, among other traits. Natural nonsynonymous genetic polymorphisms in the ovine leptin (oLEP) alter the biochemical and physiological characteristics of its gene products. Here we studied in vitro and in vivo the biochemical and physiological characteristics of recombinant hormones representing the oLEP and bovine leptin (bLEP) reference sequences of wild-type (WT) leptins (GenBank accession No. U84247 and U50365, respectively), oLEP and bLEP recombinant muteins carrying the R4C mutation, and oLEP recombinant hormones carrying the A59V and Q62R mutations, which were detected in bLEP. All proteins were purified to homogeneity as monomers and formed 1:1 molar ratio complexes with the chicken leptin-binding domain (LBD). Surface plasmon resonance experiments revealed that all protein variants exhibit reduced (P < 0.05) affinity to chicken (ch) and human (h) LBD compared with the WT oLEP and bLEP recombinant proteins. The ovine and bovine R4C muteins exhibited significantly (P < 0.05) greater induction of cell proliferation in a Baf/3 cell line bioassay, despite lower affinity toward both hLBD and chLBD. Intra-third cerebral ventricle infusion of oLEP and its 3 muteins in sheep resulted in reduced feed intake. However, the 3 tested muteins had a decreased (P < 0.05) inhibitory effect than the WT LEP. It was concluded that natural genetic polymorphisms in the bLEP are associated with variation in the biochemical and physiological properties of the protein.
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Affiliation(s)
- S Reicher
- The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
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18
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Clempson A, Pollott G, Brickell J, Bourne N, Munce N, Wathes D. Evidence that leptin genotype is associated with fertility, growth, and milk production in Holstein cows. J Dairy Sci 2011; 94:3618-28. [DOI: 10.3168/jds.2010-3626] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2010] [Accepted: 03/10/2011] [Indexed: 01/30/2023]
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Wang P, Deng L, Zhang B, Chu M, Tan Y, Fan Q, Liu C. Identification of polymorphism on leptin receptor gene of goats in southwest China. Small Rumin Res 2011. [DOI: 10.1016/j.smallrumres.2011.01.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Giblin L, Butler ST, Kearney BM, Waters SM, Callanan MJ, Berry DP. Association of bovine leptin polymorphisms with energy output and energy storage traits in progeny tested Holstein-Friesian dairy cattle sires. BMC Genet 2010; 11:73. [PMID: 20670403 PMCID: PMC2920856 DOI: 10.1186/1471-2156-11-73] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2010] [Accepted: 07/29/2010] [Indexed: 11/23/2022] Open
Abstract
Background Leptin modulates appetite, energy expenditure and the reproductive axis by signalling via its receptor the status of body energy stores to the brain. The present study aimed to quantify the associations between 10 novel and known single nucleotide polymorphisms in genes coding for leptin and leptin receptor with performance traits in 848 Holstein-Friesian sires, estimated from performance of up to 43,117 daughter-parity records per sire. Results All single nucleotide polymorphisms were segregating in this sample population and none deviated (P > 0.05) from Hardy-Weinberg equilibrium. Complete linkage disequilibrium existed between the novel polymorphism LEP-1609, and the previously identified polymorphisms LEP-1457 and LEP-580. LEP-2470 associated (P < 0.05) with milk protein concentration and calf perinatal mortality. It had a tendency to associate with milk yield (P < 0.1). The G allele of LEP-1238 was associated (P < 0.05) with reduced milk fat concentration, reduced milk protein concentration, longer gestation length and tended to associate (P < 0.1) with an increase in calving difficulty, calf perinatal mortality and somatic cells in the milk. LEP-963 exhibited an association (P < 0.05) with milk fat concentration, milk protein concentration, calving difficulty and gestation length. It also tended to associate with milk yield (P < 0.1). The R25C SNP associated (P < 0.05) with milk fat concentration, milk protein concentration, calving difficulty and length of gestation. The T allele of the Y7F SNP significantly associated with reduced angularity (P < 0.01) and reduced milk protein yield (P < 0.05). There was also a tendency (P < 0.1) for Y7F to associate with increased body condition score, reduced milk yield and shorter gestation (P < 0.1). A80V associated with reduced survival in the herd (P < 0.05). Conclusions Several leptin polymorphisms (LEP-2470, LEP-1238, LEP-963, Y7F and R25C) associated with the energetically expensive process of lactogenesis. Only SNP Y7F associated with energy storage. Associations were also observed between leptin polymorphisms and calving difficulty, gestation length and calf perinatal mortality. The lack of an association between the leptin variants investigated with calving interval in this large data set would question the potential importance of these leptin variants, or indeed leptin, in selection for improved fertility in the Holstein-Friesian dairy cow.
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Affiliation(s)
- Linda Giblin
- Teagasc, Food Research Centre, Moorepark, Fermoy, Co. Cork, Ireland.
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Li F, Chen H, Lei CZ, Ren G, Wang J, Li ZJ, Wang JQ. Novel SNPs of the bovine NUCB2 gene and their association with growth traits in three native Chinese cattle breeds. Mol Biol Rep 2010; 37:541-6. [PMID: 19728157 DOI: 10.1007/s11033-009-9732-y] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2009] [Accepted: 08/04/2009] [Indexed: 11/27/2022]
Abstract
In this study, polymorphism in the exon 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 and 11 of bovine NUCB2 gene was detected by PCR-SSCP and DNA sequencing methods in 686 individuals from three Chinese cattle breeds. Two haplotypes (M and N), three observed genotypes (MM, MN and NN) and two SNPs (NC_007313: g. 27451G>A, NC_007313: g. 27472T>C) were detected. The frequencies of haplotypes M and N in inland Chinese three breeds were 0.531-0.721 and 0.279-0.469 respectively. The studied showed that Nanyang, Jiaxian Red and Qinchuan cattle populations were in Hardy-Weinberg equilibrium at SNPs locus of NUCB2 gene (P > 0.05). Polymorphism of the NUCB2 gene was shown to be associated with growth traits in Qingchuan and Nanyang cattle breed. The linkage of two mutant sites in the bovine NUCB2 gene had significant effects on body length, body weight, heart girth, and average daily gain at 24 months (P < 0.05). Results of this study suggested that the NUCB2-gene-specific SNP may be a useful marker for growth traits in future marker-assisted selection programmes in inland Chinese cattle.
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Affiliation(s)
- F Li
- College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Molecular Biology for Agriculture, Yangling, Shaanxi, People's Republic of China
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