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Rajawat D, Nayak SS, Jain K, Sharma A, Parida S, Sahoo SP, Bhushan B, Patil DB, Dutt T, Panigrahi M. Genomic patterns of selection in morphometric traits across diverse Indian cattle breeds. Mamm Genome 2024; 35:377-389. [PMID: 39014170 DOI: 10.1007/s00335-024-10047-2] [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: 02/09/2024] [Accepted: 06/09/2024] [Indexed: 07/18/2024]
Abstract
This study seeks a comprehensive exploration of genome-wide selective processes impacting morphometric traits across diverse cattle breeds, utilizing an array of statistical methods. Morphometric traits, encompassing both qualitative and quantitative variables, play a pivotal role in characterizing and selecting livestock breeds based on their external appearance, size, and physical attributes. While qualitative traits, such as color, horn structure, and coat type, contribute to adaptive features and breed identification, quantitative traits like body weight and conformation measurements bear a closer correlation with production characteristics. This study employs advanced genotyping technologies, including the Illumina BovineSNP50 Bead Chip and next-generation sequencing methods like Reduced Representation sequencing, to identify genomic signatures associated with these traits. We applied four intra-population methods to find evidence of selection, such as Tajima's D, CLR, iHS, and ROH. We found a total of 40 genes under the selection signature, that were associated with morphometric traits in five cattle breeds (Kankrej, Tharparkar, Nelore, Sahiwal, and Gir). Crucial genes such as ADIPDQ, DPP6, INSIG1, SLC35D2 in Kankrej, LPL, ATP6V1B2, CDC14B in Tharparkar, HPSE2, PLAG1 in Nelore, PCSK1, PRKD1 in Sahiwal, and GNAQ, HPCAL1 in Gir were identified in our study. This approach provides valuable insights into the genetic basis of variations in body weight and conformation traits, facilitating informed selection processes and offering a deeper understanding of the evolutionary and domestication processes in diverse cattle breeds.
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Affiliation(s)
- Divya Rajawat
- Division of Animal Genetics, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, UP, 243122, India
| | - Sonali Sonejita Nayak
- Division of Animal Genetics, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, UP, 243122, India
| | - Karan Jain
- Division of Animal Genetics, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, UP, 243122, India
| | - Anurodh Sharma
- Division of Animal Genetics, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, UP, 243122, India
| | - Subhashree Parida
- Division of Pharmacology & Toxicology, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, UP, 243122, India
| | | | - Bharat Bhushan
- Division of Animal Genetics, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, UP, 243122, India
| | | | - Triveni Dutt
- Livestock Production and Management Section, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, UP, 243122, India
| | - Manjit Panigrahi
- Division of Animal Genetics, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, UP, 243122, India.
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Li Y, Liu T, Zhang M, Pan C, Liu X, Zhao H, Lan X. A Functional 67-bp Duplication Locating at the Core Promoter Region within the Bovine ADIPOQ Gene Is Associated with Ovarian Traits and mRNA Expression. Animals (Basel) 2024; 14:2362. [PMID: 39199896 PMCID: PMC11350689 DOI: 10.3390/ani14162362] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2024] [Revised: 08/13/2024] [Accepted: 08/14/2024] [Indexed: 09/01/2024] Open
Abstract
ADIPOQ plays a crucial role in regulating the reproductive system, but there are few reports on the effects of ADIPOQ on ovarian in dairy cows. Previous studies have verified the presence of a 67-bp mutation in the promoter region of the ADIPOQ gene. Hence, we employed ovarian tissues (n = 2111) and blood samples (n = 108) from Chinese Holstein cows as experimental samples to examine the association between ADIPOQ promoter variants and ovarian traits. We extracted DNA from these samples and conducted genetic typing identification on each sample using advanced techniques like PCR and agarose gel electrophoresis. Consequently, the DD, ID, and II genotypes were discovered. and it has been observed that the mutation frequency of this locus is low in the Chinese Holstein cow. Importantly, the correlational analysis unveiled a significant relationship (p < 0.05) between the weight of ovaries in late estrus and the width of ovaries during the estrus interval with the mutation. Result of the RT-PCR revealed that the ID genotype partially diminished the expression of the ADIPOQ gene. The results of this study suggest that the identified variable duplication could serve as a potential genetic marker for enhancing the ovarian traits of Chinese Holstein cows.
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Affiliation(s)
- Yufu Li
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China; (Y.L.); (T.L.); (M.Z.); (C.P.)
- College of Veterinary Medicine, Northwest A&F University, Yangling 712100, China;
| | - Tingting Liu
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China; (Y.L.); (T.L.); (M.Z.); (C.P.)
- School of Life Sciences, Jiangsu Normal University, Xuzhou 221008, China
| | - Mengyang Zhang
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China; (Y.L.); (T.L.); (M.Z.); (C.P.)
| | - Chuanying Pan
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China; (Y.L.); (T.L.); (M.Z.); (C.P.)
| | - Xu Liu
- College of Veterinary Medicine, Northwest A&F University, Yangling 712100, China;
| | - Haiyu Zhao
- College of Life Science, Lanzhou University, Lanzhou 730000, China
| | - Xianyong Lan
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China; (Y.L.); (T.L.); (M.Z.); (C.P.)
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AL-Jaryan IL, AL-Thuwaini TM, Al-Jebory HH. Novel variants associated with adiponectin-related traits in Awassi ewes. BENI-SUEF UNIVERSITY JOURNAL OF BASIC AND APPLIED SCIENCES 2022. [DOI: 10.1186/s43088-022-00328-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Abstract
Background
Adipose tissue secretes adiponectin (ADIPOQ), a hormone related to fat oxidation, glucose metabolism, and reproduction. The polymorphism of adiponectin is associated with productive traits in domestic animals. Thus, this study investigated the association of adiponectin gene polymorphism with lipid profile and reproductive hormones in Awassi ewe. In this study, 200 ewes between the ages of 2.5 and 5 years, neither pregnant nor lactating, were included. To determine the lipid profile and reproductive hormones, sera were separated from the blood. DNA extraction, genotyping, and sequencing reactions were used to verify the variants in the amplified fragments (exon 1).
Results
Three genotypes, CC, CA, and AA, were identified from 368 bp amplicons (exon 1). A sequencing reaction revealed a novel mutation, c.198473337C > A, in the CA genotype. The results revealed significant differences (P ≤ 0.05) in cholesterol and HDL levels in the AA genotype than CC and CA genotypes. The AA genotype had higher estradiol and progesterone levels (50.52 ± 0.64) (pg/ml) and (7.10 ± 0.04) (ng/ml), respectively, than those with the CC and CA genotypes.
Conclusions
These results conclude that the ADIPOQ gene affects lipid profiles and sex hormone levels in Awassi sheep. Choosing sheep that are polymorphic for the ADIPOQ gene should be a future study, as this gene could be linked to high prolificacy.
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Liu T, Ju X, Zhang M, Wei C, Wang D, Wang Z, Lan X, Huang XX. A 67-bp variable duplication in the promoter region of the ADIPOQ is associated with milk traits in Xinjiang brown cattle. Anim Biotechnol 2022; 33:1738-1745. [PMID: 33587650 DOI: 10.1080/10495398.2020.1868487] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Adiponectin, also known as ADIPOQ, is a hormone protein secreted by adipocytes. The ADIPOQ gene is expressed primarily in adipose tissue, and the encoded protein circulates in the bloodstream and has the potential to regulate both animal fat metabolism and hormone production. Our previous work uncovered a 67-bp variable duplication in the promoter region of ADIPOQ, which reduced the basal transcriptional activity of ADIPOQ in the 3T3_L1 cell and also inhibits the ADIPOQ mRNA expression in adipose tissue. Accordingly, the present study aimed to identify the relationship between the 67-bp structural variations in ADIPOQ promoter region and the milk traits of Xinjiang brown cattle (XJBC). The results revealed two genotypes, DD and ID, in the XJBC, and minor allelic frequency (MAF) for the 'I' allele was more than 1%. Moreover, the association analysis revealed that the 67-bp duplication in the promoter region of the ADIPOQ gene was significantly correlated with the 305 days of milk production volume, fat yield, and milk fat percentage in the XJBC (p < 0.05). These results obtained in this study suggested that the identified variable duplication could be considered as the potential genetic marker for improving milk traits of XJBC.
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Affiliation(s)
- Tingting Liu
- College of Animal Science, Xinjiang Agricultural University, Urumqi, Xinjiang, China
| | - Xing Ju
- College of Animal Science, Xinjiang Agricultural University, Urumqi, Xinjiang, China
| | - Menghua Zhang
- College of Animal Science, Xinjiang Agricultural University, Urumqi, Xinjiang, China
| | - Chen Wei
- College of Animal Science, Xinjiang Agricultural University, Urumqi, Xinjiang, China
| | - Dan Wang
- College of Animal Science, Xinjiang Agricultural University, Urumqi, Xinjiang, China
| | - Zhen Wang
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Xianyong Lan
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Xi-Xia Huang
- College of Animal Science, Xinjiang Agricultural University, Urumqi, Xinjiang, China
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de Araújo TLAC, Feijó GLD, Neves AP, Nogueira É, de Oliveira LOF, Gomes MDNB, do Egito AA, Ferraz ALJ, Menezes GRDO, Latta KI, Ferreira JR, Vieira DG, Pereira ES, Gomes RDC. Effect of genetic merit for backfat thickness and paternal breed on performance, carcass traits, and gene expression in subcutaneous adipose tissue of feedlot-finished steers. Livest Sci 2022. [DOI: 10.1016/j.livsci.2022.104998] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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An Q, Zhou H, Hu J, Luo Y, Hickford JGH. Haplotypes of the Ovine Adiponectin Gene and Their Association with Growth and Carcass Traits in New Zealand Romney Lambs. Genes (Basel) 2017; 8:E160. [PMID: 28604630 PMCID: PMC5485524 DOI: 10.3390/genes8060160] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Revised: 05/26/2017] [Accepted: 06/03/2017] [Indexed: 12/24/2022] Open
Abstract
Adiponectin plays an important role in energy homeostasis and metabolism in mammalian adipose tissue. In this study, the relationship between adiponectin gene (ADIPOQ) haplotypes and variation in growth and carcass traits in New Zealand (NZ) Romney lambs was investigated using General Linear Models (GLMs). Eight haplotypes were found in these lambs and they were composed of the four previously reported promoter fragment sequences (A₁-D₁) and three previously reported intron 2-exon 3 sequences (A₃-C₃). The frequencies of the haplotypes ranged from 0.07% to 45.91%. The presence of A₁-A₃ was associated with a decreased pre-weaning growth rate (p = 0.037), and decreased leg lean-meat yield (p = 0.001), loin lean-meat yield (p = 0.018) and total lean-meat yield (p = 0.004). The presence of A₁-C₃ was associated with increased carcass fat depth over the 12th rib (V-GR; p = 0.001) and a decreased proportion of loin lean-meat yield (p = 0.045). The presence of B₁-A₃ was associated with an increased proportion of leg lean-meat yield (p = 0.016) and proportion of shoulder lean-meat yield (p = 0.030). No associations were found with birth weight, tailing weight and weaning weight. These results suggest that ovine ADIPOQ may have value as a genetic marker for NZ Romney sheep breeding.
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Affiliation(s)
- Qingming An
- Faculty of Wujiang, Tongren University, Tongren 554300, China.
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China.
| | - Huitong Zhou
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China.
- Gene-Marker Laboratory, Faculty of Agriculture and Life Sciences, PO Box 84, Lincoln University, Lincoln 7646, New Zealand.
| | - Jiang Hu
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China.
| | - Yuzhu Luo
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China.
| | - Jon G H Hickford
- Gene-Marker Laboratory, Faculty of Agriculture and Life Sciences, PO Box 84, Lincoln University, Lincoln 7646, New Zealand.
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Pareek CS, Smoczyński R, Kadarmideen HN, Dziuba P, Błaszczyk P, Sikora M, Walendzik P, Grzybowski T, Pierzchała M, Horbańczuk J, Szostak A, Ogluszka M, Zwierzchowski L, Czarnik U, Fraser L, Sobiech P, Wąsowicz K, Gelfand B, Feng Y, Kumar D. Single Nucleotide Polymorphism Discovery in Bovine Pituitary Gland Using RNA-Seq Technology. PLoS One 2016; 11:e0161370. [PMID: 27606429 PMCID: PMC5015895 DOI: 10.1371/journal.pone.0161370] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2016] [Accepted: 08/04/2016] [Indexed: 01/14/2023] Open
Abstract
Examination of bovine pituitary gland transcriptome by strand-specific RNA-seq allows detection of putative single nucleotide polymorphisms (SNPs) within potential candidate genes (CGs) or QTLs regions as well as to understand the genomics variations that contribute to economic trait. Here we report a breed-specific model to successfully perform the detection of SNPs in the pituitary gland of young growing bulls representing Polish Holstein-Friesian (HF), Polish Red, and Hereford breeds at three developmental ages viz., six months, nine months, and twelve months. A total of 18 bovine pituitary gland polyA transcriptome libraries were prepared and sequenced using the Illumina NextSeq 500 platform. Sequenced FastQ databases of all 18 young bulls were submitted to NCBI-SRA database with NCBI-SRA accession numbers SRS1296732. For the investigated young bulls, a total of 113,882,3098 raw paired-end reads with a length of 156 bases were obtained, resulting in an approximately 63 million paired-end reads per library. Breed-wise, a total of 515.38, 215.39, and 408.04 million paired-end reads were obtained for Polish HF, Polish Red, and Hereford breeds, respectively. Burrows-Wheeler Aligner (BWA) read alignments showed 93.04%, 94.39%, and 83.46% of the mapped sequencing reads were properly paired to the Polish HF, Polish Red, and Hereford breeds, respectively. Constructed breed-specific SNP-db of three cattle breeds yielded at 13,775,885 SNPs. On an average 765,326 breed-specific SNPs per young bull were identified. Using two stringent filtering parameters, i.e., a minimum 10 SNP reads per base with an accuracy ≥ 90% and a minimum 10 SNP reads per base with an accuracy = 100%, SNP-db records were trimmed to construct a highly reliable SNP-db. This resulted in a reduction of 95,7% and 96,4% cut-off mark of constructed raw SNP-db. Finally, SNP discoveries using RNA-Seq data were validated by KASP™ SNP genotyping assay. The comprehensive QTLs/CGs analysis of 76 QTLs/CGs with RNA-seq data identified KCNIP4, CCSER1, DPP6, MAP3K5 and GHR CGs with highest SNPs hit loci in all three breeds and developmental ages. However, CAST CG with more than 100 SNPs hits were observed only in Polish HF and Hereford breeds.These findings are important for identification and construction of novel tissue specific SNP-db and breed specific SNP-db dataset by screening of putative SNPs according to QTL db and candidate genes for bovine growth and reproduction traits, one can develop genomic selection strategies for growth and reproductive traits.
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Affiliation(s)
- Chandra Shekhar Pareek
- Division of Functional Genomics in Biological and Biomedical Research, Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University, Torun, Poland
- * E-mail:
| | - Rafał Smoczyński
- Division of Functional Genomics in Biological and Biomedical Research, Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University, Torun, Poland
| | - Haja N. Kadarmideen
- Department of Large Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Piotr Dziuba
- Division of Functional Genomics in Biological and Biomedical Research, Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University, Torun, Poland
| | - Paweł Błaszczyk
- Division of Functional Genomics in Biological and Biomedical Research, Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University, Torun, Poland
| | - Marcin Sikora
- Division of Functional Genomics in Biological and Biomedical Research, Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University, Torun, Poland
| | - Paulina Walendzik
- Division of Functional Genomics in Biological and Biomedical Research, Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University, Torun, Poland
| | - Tomasz Grzybowski
- Ludwik Rydygier Collegium Medicum, Institute of Forensic Medicine, Department of Molecular and Forensic Genetics, The Nicolaus Copernicus University, Bydgoszcz, Poland
| | - Mariusz Pierzchała
- Institute of Genetics and Animal Breeding of the Polish Academy of Sciences, Jastrzebiec, Poland
| | - Jarosław Horbańczuk
- Institute of Genetics and Animal Breeding of the Polish Academy of Sciences, Jastrzebiec, Poland
| | - Agnieszka Szostak
- Institute of Genetics and Animal Breeding of the Polish Academy of Sciences, Jastrzebiec, Poland
| | - Magdalena Ogluszka
- Institute of Genetics and Animal Breeding of the Polish Academy of Sciences, Jastrzebiec, Poland
| | - Lech Zwierzchowski
- Institute of Genetics and Animal Breeding of the Polish Academy of Sciences, Jastrzebiec, Poland
| | - Urszula Czarnik
- Faculty of Animal Bio-engineering, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland
| | - Leyland Fraser
- Faculty of Animal Bio-engineering, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland
| | - Przemysław Sobiech
- Faculty of Veterinary Medicine, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland
| | - Krzysztof Wąsowicz
- Faculty of Veterinary Medicine, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland
| | - Brian Gelfand
- Waksman Institute of Microbiology, Rutgers, The State University of New Jersey, Piscataway, New Jersey, United States of America
| | - Yaping Feng
- Waksman Institute of Microbiology, Rutgers, The State University of New Jersey, Piscataway, New Jersey, United States of America
| | - Dibyendu Kumar
- Waksman Institute of Microbiology, Rutgers, The State University of New Jersey, Piscataway, New Jersey, United States of America
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Kwon A, Srikanth K, Lee E, Kim S, Chung H. Confirmation of genotypic effects for the bovine APM1 gene on marbling in Hanwoo cattle. JOURNAL OF ANIMAL SCIENCE AND TECHNOLOGY 2016; 58:15. [PMID: 27054043 PMCID: PMC4822224 DOI: 10.1186/s40781-016-0096-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/25/2015] [Accepted: 03/23/2016] [Indexed: 01/04/2023]
Abstract
Background Our previous study had identified the SNP (g.81966377T > C) and indel (g.81966364D > I) located in the promoter of APM1 to have a significant effect on marbling in Hanwoo. APM1 encodes an adipocytokine called adiponectin, which plays a significant role in lipogenesis. The aim of this study was to verify and validate the effect of the SNP and indel on marbling and other carcass traits in a large, representative, countrywide population of Hanwoo cattle. The carcass traits measured were marbling (MAR), backfat thickness (BFT), loin eye area (LEA), and carcass weight (CAW). Results Primers were designed to amplify 346 bp of the genomic segment that contained the targeted SNP (g.81966377) and the indel (g.81966364). After data curation, the genotypes of 8,378 individuals identified using direct sequencing analysis estimated frequencies for C (0.686) and T (0.314) respectively showing genotype frequencies for CC (0.470), CT (0.430) and TT (0.098). The genotypes were significantly associated with MAR, BFT and LEA. The indel had significant effect on marbling (P < .0001) with strong additive genetic effects. The allele frequencies was estimated at (DEL, 0.864) and insertion (INS, 0.136) presenting genotypes of D/D (75.63 %), D/I (21.44 %), and I/I (2.92 %). Significant departure from Hardy-Weinberg equilibrium was not detected for both the SNP and the indel. Conclusion The SNP genotypes showed significant association with MAR, BFT and LEA with strong additive genetic effects, while the indel was significantly associated with MAR. The results confirmed that the variants can be used as a genetic marker for improving marbling in Hanwoo.
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Affiliation(s)
- Anam Kwon
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, Wanju, Jeonbuk, 565-851 Republic of Korea
| | - Krishnamoorthy Srikanth
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, Wanju, Jeonbuk, 565-851 Republic of Korea
| | - Eunjin Lee
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, Wanju, Jeonbuk, 565-851 Republic of Korea
| | - Seonkwan Kim
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, Wanju, Jeonbuk, 565-851 Republic of Korea
| | - Hoyoung Chung
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, Wanju, Jeonbuk, 565-851 Republic of Korea
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Haplotypes and Sequence Variation in the Ovine Adiponectin Gene (ADIPOQ). Genes (Basel) 2015; 6:1230-41. [PMID: 26610572 PMCID: PMC4690037 DOI: 10.3390/genes6041230] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2015] [Revised: 10/28/2015] [Accepted: 11/03/2015] [Indexed: 11/17/2022] Open
Abstract
The adiponectin gene (ADIPOQ) plays an important role in energy homeostasis. In this study five separate regions (regions 1 to 5) of ovine ADIPOQ were analysed using PCR-SSCP. Four different PCR-SSCP patterns (A1-D1, A2-D2) were detected in region-1 and region-2, respectively, with seven and six SNPs being revealed. In region-3, three different patterns (A3-C3) and three SNPs were observed. Two patterns (A4-B4, A5-B5) and two and one SNPs were observed in region-4 and region-5, respectively. In total, nineteen SNPs were detected, with five of them in the coding region and two (c.46T/C and c.515G/A) putatively resulting in amino acid changes (p.Tyr16His and p.Lys172Arg). In region-1, -2 and -3 of 316 sheep from eight New Zealand breeds, variants A1, A2 and A3 were the most common, although variant frequencies differed in the eight breeds. Across region-1 and region-3, nine haplotypes were identified and haplotypes A1-A3, A1-C3, B1-A3 and B1-C3 were most common. These results indicate that the ADIPOQ gene is polymorphic and suggest that further analysis is required to see if the variation in the gene is associated with animal production traits.
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Paredes-Sánchez FA, Sifuentes-Rincón AM, Segura Cabrera A, García Pérez CA, Parra Bracamonte GM, Ambriz Morales P. Associations of SNPs located at candidate genes to bovine growth traits, prioritized with an interaction networks construction approach. BMC Genet 2015. [PMID: 26198337 PMCID: PMC4511253 DOI: 10.1186/s12863-015-0247-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Background For most domestic animal species, including bovines, it is difficult to identify causative genetic variants involved in economically relevant traits. The candidate gene approach is efficient because it investigates genes that are expected to be associated with the expression of a trait and defines whether the genetic variation present in a population is associated with phenotypic diversity. A potential limitation of this approach is the identification of candidates. This study used a bioinformatics approach to identify candidate genes via a search guided by a functional interaction network. Results A functional interaction network tool, BosNet, was constructed for Bos taurus. Predictions for candidate genes were performed using the guilt-by-association principle in BosNet. Association analyses identified five novel markers within BosNet-prioritized genes that had significant effects on different growth traits in Charolais and Brahman cattle. Conclusions BosNet is an excellent tool for the identification of single nucleotide polymorphisms that are potentially associated with complex traits.
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Affiliation(s)
- Francisco Alejandro Paredes-Sánchez
- Laboratorio de Biotecnología Animal, Centro de Biotecnología Genómica. IPN, Boulevard del Maestro esq. Elías Piña, Col. Narciso Mendoza, Cd. Reynosa, Tam, C.P. 88710, Mexico.
| | - Ana María Sifuentes-Rincón
- Laboratorio de Biotecnología Animal, Centro de Biotecnología Genómica. IPN, Boulevard del Maestro esq. Elías Piña, Col. Narciso Mendoza, Cd. Reynosa, Tam, C.P. 88710, Mexico.
| | - Aldo Segura Cabrera
- Red de Estudios Moleculares Avanzados, Instituto de Ecología, A.C., Xalapa, Mexico.
| | - Carlos Armando García Pérez
- Laboratorio de Bioinformática, Centro de Biotecnología Genómica. IPN, Boulevard del Maestro esq. Elías Piña, Col. Narciso Mendoza, Cd. Reynosa, Tam, C.P. 88710, Mexico.
| | - Gaspar Manuel Parra Bracamonte
- Laboratorio de Biotecnología Animal, Centro de Biotecnología Genómica. IPN, Boulevard del Maestro esq. Elías Piña, Col. Narciso Mendoza, Cd. Reynosa, Tam, C.P. 88710, Mexico.
| | - Pascuala Ambriz Morales
- Laboratorio de Biotecnología Animal, Centro de Biotecnología Genómica. IPN, Boulevard del Maestro esq. Elías Piña, Col. Narciso Mendoza, Cd. Reynosa, Tam, C.P. 88710, Mexico.
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11
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Choi Y, Davis ME, Chung H. Effects of genetic variants in the promoter region of the bovine adiponectin (ADIPOQ) gene on marbling of Hanwoo beef cattle. Meat Sci 2015; 105:57-62. [DOI: 10.1016/j.meatsci.2015.02.014] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2014] [Revised: 12/19/2014] [Accepted: 02/24/2015] [Indexed: 12/18/2022]
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Fonseca PDDS, de Souza FRP, de Camargo GMF, Gil FMM, Cardoso DF, Zetouni L, Braz CU, Boligon AA, Branco RH, de Albuquerque LG, Mercadante MEZ, Tonhati H. Association of ADIPOQ, OLR1 and PPARGC1A gene polymorphisms with growth and carcass traits in Nelore cattle. Meta Gene 2015; 4:1-7. [PMID: 25853056 PMCID: PMC4354916 DOI: 10.1016/j.mgene.2015.02.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2014] [Revised: 01/12/2015] [Accepted: 02/04/2015] [Indexed: 01/19/2023] Open
Abstract
In beef cattle farming, growth and carcass traits are important for genetic breeding programs. Molecular markers can be used to assist selection and increase genetic gain. The ADIPOQ, OLR1 and PPARGC1A genes are involved in lipid synthesis and fat accumulation in adipose tissue. The objective of this study was to identify polymorphisms in these genes and to assess the association with growth and carcass traits in Nelore cattle. A total of 639 animals were genotyped by PCR-RFLP for rs208549452, rs109019599 and rs109163366 in ADIPOQ, OLR1 and PPARGC1A gene, respectively. We analyzed the association of SNPs identified with birth weight, weaning weight, female yearling weight, female hip height, male yearling weight, male hip height, loin eye area, rump fat thickness, and backfat thickness. The OLR1 marker was associated with rump fat thickness and weaning weight (P < 0.05) and the PPARGC1 marker was associated with female yearling weight.
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Affiliation(s)
- Patrícia D da S Fonseca
- Universidade Estadual Paulista (Unesp), Departamento de Zootecnia, Jaboticabal, SP 14884-900, Brazil
| | - Fábio R P de Souza
- Universidade Federal de Pelotas (UFPel), Departamento de Ecologia, Zoologia e Genética, Pelotas, RS 96010-900, Brazil
| | - Gregório M F de Camargo
- Universidade Estadual Paulista (Unesp), Departamento de Zootecnia, Jaboticabal, SP 14884-900, Brazil
| | - Fernanda M M Gil
- Universidade Estadual Paulista (Unesp), Departamento de Zootecnia, Jaboticabal, SP 14884-900, Brazil
| | - Diercles F Cardoso
- Universidade Estadual Paulista (Unesp), Departamento de Zootecnia, Jaboticabal, SP 14884-900, Brazil
| | - Larissa Zetouni
- Universidade Estadual Paulista (Unesp), Departamento de Zootecnia, Jaboticabal, SP 14884-900, Brazil
| | - Camila U Braz
- Universidade Estadual Paulista (Unesp), Departamento de Zootecnia, Jaboticabal, SP 14884-900, Brazil
| | - Arione A Boligon
- Universidade Federal de Pelotas (UFPel), Departamento de Zootecnia, Pelotas, RS 96010-900, Brazil
| | - Renata H Branco
- Instituto de Zootecnia, Centro APTA Bovinos de Corte, Sertãozinho, SP, Brazil
| | - Lucia G de Albuquerque
- Universidade Estadual Paulista (Unesp), Departamento de Zootecnia, Jaboticabal, SP 14884-900, Brazil
| | | | - Humberto Tonhati
- Universidade Estadual Paulista (Unesp), Departamento de Zootecnia, Jaboticabal, SP 14884-900, Brazil
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13
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Feng X, Yu X, Pang M, Liu H, Tong J. Molecular characterization and expression of three preprosomatostatin genes and their association with growth in common carp (Cyprinus carpio). Comp Biochem Physiol B Biochem Mol Biol 2014; 182:37-46. [PMID: 25536408 DOI: 10.1016/j.cbpb.2014.12.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2014] [Revised: 12/12/2014] [Accepted: 12/13/2014] [Indexed: 12/21/2022]
Abstract
Somatostatins (SSs) are a structurally diverse family of peptides that play important roles in the regulation of growth, development and metabolism in vertebrates. In this study, three preprosomatostatin genes (PSSs) in the common carp, Cyprinus carpio (Cc) were identified and characterized. Based on cloned sequences and genome BLAST, six isoforms of the PSS gene in C. carpio (CcPSS) were identified and included CcPSS1a and CcPSS1b, CcPSS2a and CcPSS2b, and finally, CcPSS3a and CcPSS3b. The open reading frames (ORF) of CcPSS1a, CcPSS2a and CcPSS3a consist of 345, 336 and 363 nucleotides. During embryonic development, the expressions of CcPSS2 and CcPSS3 were first observed at the stage of optic vesicle, and CcPSS1 mRNA was initially detected at the stage of muscular effect. The highest mRNA levels of CcPSS1, CcPSS2 and CcPSS3 were observed at 1-day post-hatch (dph), 2-dph and the stage of heart beating, respectively. In the adult brain, the distributions of three CcPSS mRNAs were differential but overlapping in the hypothalamus, telencephalon and medulla oblongata. For peripheral tissues, all three CcPSS mRNAs were detected in the mid-intestine, and CcPSS1 and CcPSS3 mRNAs were also expressed in the liver. Owing to the importance of somatostatins on regulating growth, functional mutations of CcPSSs were identified in a C. carpio population. A total of 23 polymorphic sites were detected in CcPSS1a and CcPSS3a. Of them, two SNPs (CcPSS1a-g.922C>T, and CcPSS3a-g.1125C>A) were significantly associated with growth traits, indicating their potential applications in gene (marker)-assisted selective breeding in C. carpio.
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Affiliation(s)
- Xiu Feng
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, The Chinese Academy of Sciences, Wuhan 430072, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaomu Yu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, The Chinese Academy of Sciences, Wuhan 430072, China
| | - Meixia Pang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, The Chinese Academy of Sciences, Wuhan 430072, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Haiyang Liu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, The Chinese Academy of Sciences, Wuhan 430072, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jingou Tong
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, The Chinese Academy of Sciences, Wuhan 430072, China.
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14
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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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15
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Allais S, Levéziel H, Hocquette JF, Rousset S, Denoyelle C, Journaux L, Renand G. Fine mapping of quantitative trait loci underlying sensory meat quality traits in three French beef cattle breeds. J Anim Sci 2014; 92:4329-41. [PMID: 25149327 DOI: 10.2527/jas.2014-7868] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Improving the traits that underlie meat quality is a major challenge in the beef industry. The objective of this paper was to detect QTL linked to sensory meat quality traits in 3 French beef cattle breeds. We genotyped 1,059, 1,219, and 947 young bulls and their sires belonging to the Charolais, Limousin, and Blonde d'Aquitaine breeds, respectively, using the Illumina BovineSNP50 BeadChip (Illumina Inc., San Diego, CA). After estimating relevant genetic parameters using VCE software, we performed a linkage disequilibrium and linkage analysis on 4 meat traits: intramuscular fat content, muscle lightness, shear force, and tenderness score. Heritability coefficients largely ranged between 0.10 and 0.24; however, they reached a maximum of 0.44 and 0.50 for intramuscular fat content and tenderness score, respectively, in the Charolais breed. The 2 meat texture traits, shear force and tenderness score, were strongly genetically correlated (-0.91 in the Charolais and Limousin breed and -0.86 in the Blonde d'Aquitaine breed), indicating that they are 2 different measures of approximately the same trait. The genetic correlation between tenderness and intramuscular fat content differed across breeds. Using a significance threshold of 5 × 10(-4) for QTL detection, we found more than 200 significant positions across the 29 autosomal chromosomes for the 4 traits in the Charolais and Blonde d'Aquitaine breeds; in contrast, there were only 78 significant positions in the Limousin breed. Few QTL were common across breeds. We detected QTL for intramuscular fat content located near the myostatin gene in the Charolais and Blonde d'Aquitaine breeds. No mutation in this gene has been reported for the Blonde d'Aquitaine breed; therefore, it suggests that an unknown mutation could be segregating in this breed. We confirmed that, in certain breeds, markers in the calpastatin and calpain 1 gene regions affect tenderness. We also found new QTL as several QTL on chromosome 3 that are significantly associated with meat tenderness in the Blonde d'Aquitaine breed. Overall, these results greatly contribute to the goal of building a panel of markers that can be used to select animals of high meat quality.
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Affiliation(s)
- S Allais
- INRA, AgroParisTech, UMR1313 Unité de Génétique Animale et Biologie Intégrative, F-78350 Jouy-en-Josas, France Union Nationale des Coopératives agricoles d'Elevage et d'Insémination Animale, F-75595 Paris Cedex 12, France
| | - H Levéziel
- INRA, Université de Limoges, UMR1061 Unité de Génétique Moléculaire Animale, F-87060 Limoges, France
| | - J F Hocquette
- INRA, VetAgro Sup, UMR1213, Recherches sur les Herbivores, F-63122 Saint Genès Champanelle, France
| | - S Rousset
- INRA, Clermont Université, UMR1019 Unité de Nutrition Humaine, Centre de Recherches en Nutrition Humaine d'Auvergne, F-63001 Clermont-Ferrand, France
| | - C Denoyelle
- Institut de l'Elevage, F-75595 Paris Cedex 12, France
| | - L Journaux
- Institut de l'Elevage, F-75595 Paris Cedex 12, France
| | - G Renand
- INRA, Clermont Université, UMR1019 Unité de Nutrition Humaine, Centre de Recherches en Nutrition Humaine d'Auvergne, F-63001 Clermont-Ferrand, France
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16
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Zhang L, Yang M, Li C, Xu Y, Sun J, Lei C, Lan X, Zhang C, Chen H. Identification and genetic effect of a variable duplication in the promoter region of the cattleADIPOQgene. Anim Genet 2013; 45:171-9. [DOI: 10.1111/age.12112] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/21/2013] [Indexed: 11/30/2022]
Affiliation(s)
- L. Zhang
- College of Animal Science and Technology; Northwest A & F University; Shaanxi Key Laboratory of Molecular Biology for Agriculture; Yangling Shaanxi 712100 China
| | - M. Yang
- College of Animal Science and Technology; Northwest A & F University; Shaanxi Key Laboratory of Molecular Biology for Agriculture; Yangling Shaanxi 712100 China
| | - C. Li
- United States Department of Agriculture-Agricultural Research Service; Bovine Functional Genomics Laboratory; Beltsville MD 20705 USA
| | - Y. Xu
- College of Animal Science and Technology; Northwest A & F University; Shaanxi Key Laboratory of Molecular Biology for Agriculture; Yangling Shaanxi 712100 China
| | - J. Sun
- College of Animal Science and Technology; Northwest A & F University; Shaanxi Key Laboratory of Molecular Biology for Agriculture; Yangling Shaanxi 712100 China
| | - C. Lei
- College of Animal Science and Technology; Northwest A & F University; Shaanxi Key Laboratory of Molecular Biology for Agriculture; Yangling Shaanxi 712100 China
| | - X. Lan
- College of Animal Science and Technology; Northwest A & F University; Shaanxi Key Laboratory of Molecular Biology for Agriculture; Yangling Shaanxi 712100 China
| | - C. Zhang
- Institute of Cellular and Molecular Biology; Jiangsu Normal University; Xuzhou Jiangsu 221116 China
| | - H. Chen
- College of Animal Science and Technology; Northwest A & F University; Shaanxi Key Laboratory of Molecular Biology for Agriculture; Yangling Shaanxi 712100 China
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17
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Zhang L, Li M, Lai X, Yang M, Xu Y, Hua L, Lan X, Zhang C, Chen H. Haplotype combination of polymorphisms in the ADIPOQ gene promoter is associated with growth traits in Qinchuan cattle. Genome 2013; 56:389-94. [PMID: 24099391 DOI: 10.1139/gen-2013-0054] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Adiponectin modulates lipid and glucose metabolism in adipose tissues and is also related to bone metabolism. Polymorphisms in the ADIPOQ gene likely have an impact on growth traits in cattle. In this study, we examined the relationship between ADIPOQ polymorphisms and body measurement parameters in Chinese beef cattle. First, we sequenced ADIPOQ and 1.2 kb of DNA upstream of its promoter, and we found 14 polymorphisms. With the luciferase reporter assay, we showed that the two polymorphisms SNP PR_-135 A>G and PR_-68 G>C, which are located in the core region of promoter, influence promoter activity of ADIPOQ. Second, we identified three haplotypes involved in these two polymorphic sites: A (A-135/C-68), B (A-135/G-68), and C (G-135/G-68). Haplotypes B and C are major haplotypes in five Chinese populations of cattle (Qinchuan, Nanyang, Jiaxian, Hazakh, and Chinese Holstein). We studied the effects of these three haplotypes on body measurements, gene expression, and promoter activity, and we found that the genotypes are associated with body measurement parameters in Qinchuan cattle. Individuals with genotype BC (AG/GG) had significantly higher body height and heart girth than others, and this result may be interpreted by the following two observations. The promoter activity with haplotype B (A/G) is significantly higher than those with A (A/C) and C (G/G) in driving reporter gene transcription; the ADIPOQ mRNA level in cattle with genotype BC (AG/GG) is relatively lower than that in cattle with genotype BB (AA/GG).
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Affiliation(s)
- Liangzhi Zhang
- a College of Animal Science and Technology, Northwest A & F University, Shaanxi Key Laboratory of Molecular Biology for Agriculture, Yangling, Shaanxi, P.R. China
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18
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Novel SNPs in the bovine ADIPOQ and PPARGC1A genes are associated with carcass traits in Hanwoo (Korean cattle). Mol Biol Rep 2013; 40:4651-60. [DOI: 10.1007/s11033-013-2560-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2012] [Accepted: 04/29/2013] [Indexed: 12/16/2022]
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19
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Metzger J, Schrimpf R, Philipp U, Distl O. Expression levels of LCORL are associated with body size in horses. PLoS One 2013; 8:e56497. [PMID: 23418579 PMCID: PMC3572084 DOI: 10.1371/journal.pone.0056497] [Citation(s) in RCA: 81] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2012] [Accepted: 01/10/2013] [Indexed: 01/24/2023] Open
Abstract
Body size is an important characteristic for horses of various breeds and essential for the classification of ponies concerning the limit value of 148 cm (58.27 inches) height at the withers. Genome-wide association analyses revealed the highest associated quantitative trait locus for height at the withers on horse chromosome (ECA) 3 upstream of the candidate gene LCORL. Using 214 Hanoverian horses genotyped on the Illumina equine SNP50 BeadChip and 42 different horse breeds across all size ranges, we confirmed the highly associated single nucleotide polymorphism BIEC2-808543 (−log10P = 8.3) and the adjacent gene LCORL as the most promising candidate for body size. We investigated the relative expression levels of LCORL and its two neighbouring genes NCAPG and DCAF16 using quantitative real-time PCR (RT-qPCR). We could demonstrate a significant association of the relative LCORL expression levels with the size of the horses and the BIEC2-808543 genotypes within and across horse breeds. In heterozygous C/T-horses expression levels of LCORL were significantly decreased by 40% and in homozygous C/C-horses by 56% relative to the smaller T/T-horses. Bioinformatic analyses indicated that this SNP T>C mutation is disrupting a putative binding site of the transcription factor TFIID which is important for the transcription process of genes involved in skeletal bone development. Thus, our findings suggest that expression levels of LCORL play a key role for body size within and across horse breeds and regulation of the expression of LCORL is associated with genetic variants of BIEC2-808543. This is the first functional study for a body size regulating polymorphism in horses and a further step to unravel the mechanisms for understanding the genetic regulation of body size in horses.
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Affiliation(s)
- Julia Metzger
- Institute for Animal Breeding and Genetics, University of Veterinary Medicine Hannover, Hannover, Germany
| | - Rahel Schrimpf
- Institute for Animal Breeding and Genetics, University of Veterinary Medicine Hannover, Hannover, Germany
| | - Ute Philipp
- Institute for Animal Breeding and Genetics, University of Veterinary Medicine Hannover, Hannover, Germany
| | - Ottmar Distl
- Institute for Animal Breeding and Genetics, University of Veterinary Medicine Hannover, Hannover, Germany
- * E-mail:
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20
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Kim KS, Kim SW, Raney NE, Ernst CW. Evaluation of BTA1 and BTA5 QTL Regions for Growth and Carcass Traits in American and Korean Cattle. ASIAN-AUSTRALASIAN JOURNAL OF ANIMAL SCIENCES 2012; 25:1521-8. [PMID: 25049512 PMCID: PMC4093042 DOI: 10.5713/ajas.2012.12218] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 04/23/2012] [Revised: 08/17/2012] [Accepted: 06/07/2012] [Indexed: 11/30/2022]
Abstract
Previously identified QTL regions on BTA1 and BTA5 were investigated to validate the QTL regions and to identify candidate genes for growth and carcass traits in commercial cattle populations from the USA and Korea. Initially, a total of 8 polymorphic microsatellite (MS) markers in the BTA1 and 5 QTL regions were used for Chi-square tests to compare the frequencies of individual alleles between high and low phenotypic groups for the US (Michigan Cattleman’s Association/Michigan State University; MCA/MSU) cattle. For a subsequent study, 24 candidate genes containing missense mutations and located within the QTL regions based on bovine genome sequence data were analyzed for genotyping in the two commercial cattle populations. Re-sequencing analyses confirmed 18 public missense SNPs and identified 9 new SNPs. Seventeen of these SNPs were used for genotyping of the MCA/MSU cattle (n = 98) and Korean native cattle (n = 323). On BTA1, UPK1B, HRG, and MAGEF1 polymorphisms residing between BM1312 and BMS4048 were significantly associated with growth and carcass traits in one or both of the MCA/MSU and Korean populations. On BTA5, ABCD2, IL22 and SNRPF polymorphisms residing between BL4 and BR2936 were associated with marbling and backfat traits in one or both of the MCA/MSU and Korean cattle populations. These results suggested that BTA 1 and 5 QTL regions may be segregating in both Korean Hanwoo and USA commercial cattle populations and DNA markers tested in this study may contribute to the identification of positional candidate genes for marker-assisted selection programs.
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Affiliation(s)
- K S Kim
- Department of Animal Science, Michigan State University, East Lansing, MI 48824, USA
| | - S W Kim
- Department of Animal Science, Michigan State University, East Lansing, MI 48824, USA
| | - N E Raney
- Department of Animal Science, Michigan State University, East Lansing, MI 48824, USA
| | - C W Ernst
- Department of Animal Science, Michigan State University, East Lansing, MI 48824, USA
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21
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Barendse W. Haplotype analysis improved evidence for candidate genes for intramuscular fat percentage from a genome wide association study of cattle. PLoS One 2011; 6:e29601. [PMID: 22216329 PMCID: PMC3247274 DOI: 10.1371/journal.pone.0029601] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2011] [Accepted: 12/01/2011] [Indexed: 11/23/2022] Open
Abstract
In genome wide association studies (GWAS), haplotype analyses of SNP data are neglected in favour of single point analysis of associations. In a recent GWAS, we found that none of the known candidate genes for intramuscular fat (IMF) had been identified. In this study, data from the GWAS for these candidate genes were re-analysed as haplotypes. First, we confirmed that the methodology would find evidence for association between haplotypes in candidate genes of the calpain-calpastatin complex and musculus longissimus lumborum peak force (LLPF), because these genes had been confirmed through single point analysis in the GWAS. Then, for intramuscular fat percent (IMF), we found significant partial haplotype substitution effects for the genes ADIPOQ and CXCR4, as well as suggestive associations to the genes CEBPA, FASN, and CAPN1. Haplotypes for these genes explained 80% more of the phenotypic variance compared to the best single SNP. For some genes the analyses suggested that there was more than one causative mutation in some genes, or confirmed that some causative mutations are limited to particular subgroups of a species. Fitting the SNPs and their interactions simultaneously explained a similar amount of the phenotypic variance compared to haplotype analyses. Haplotype analysis is a neglected part of the suite of tools used to analyse GWAS data, would be a useful method to extract more information from these data sets, and may contribute to reducing the missing heritability problem.
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Affiliation(s)
- William Barendse
- Cooperative Research Centre for Beef Genetic Technologies, Commonwealth Scientific and Industrial Research Organization, St. Lucia, Queensland, Australia.
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22
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Shin SC, Heo JP, Chung ER. Genetic variants of the FABP4 gene are associated with marbling scores and meat quality grades in Hanwoo (Korean cattle). Mol Biol Rep 2011; 39:5323-30. [DOI: 10.1007/s11033-011-1331-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2011] [Accepted: 12/03/2011] [Indexed: 12/16/2022]
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23
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Rolf MM, Taylor JF, Schnabel RD, McKay SD, McClure MC, Northcutt SL, Kerley MS, Weaber RL. Genome-wide association analysis for feed efficiency in Angus cattle. Anim Genet 2011; 43:367-74. [PMID: 22497295 PMCID: PMC3437496 DOI: 10.1111/j.1365-2052.2011.02273.x] [Citation(s) in RCA: 81] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Estimated breeding values for average daily feed intake (AFI; kg/day), residual feed intake (RFI; kg/day) and average daily gain (ADG; kg/day) were generated using a mixed linear model incorporating genomic relationships for 698 Angus steers genotyped with the Illumina BovineSNP50 assay. Association analyses of estimated breeding values (EBVs) were performed for 41 028 single nucleotide polymorphisms (SNPs), and permutation analysis was used to empirically establish the genome-wide significance threshold (P < 0.05) for each trait. SNPs significantly associated with each trait were used in a forward selection algorithm to identify genomic regions putatively harbouring genes with effects on each trait. A total of 53, 66 and 68 SNPs explained 54.12% (24.10%), 62.69% (29.85%) and 55.13% (26.54%) of the additive genetic variation (when accounting for the genomic relationships) in steer breeding values for AFI, RFI and ADG, respectively, within this population. Evaluation by pathway analysis revealed that many of these SNPs are in genomic regions that harbour genes with metabolic functions. The presence of genetic correlations between traits resulted in 13.2% of SNPs selected for AFI and 4.5% of SNPs selected for RFI also being selected for ADG in the analysis of breeding values. While our study identifies panels of SNPs significant for efficiency traits in our population, validation of all SNPs in independent populations will be necessary before commercialization.
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Affiliation(s)
- M M Rolf
- Division of Animal Sciences, University of Missouri, Columbia, 65211, USA.
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24
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Lan XY, Liu JB, Zhu JL, Liu TG, Zhang LZ, Zhang Y, Lei CZ, Chen H. Identification of a novel mutation within the goat adiponectin gene and its effect on body weight in Chinese indigenous breeds. Biochem Genet 2011; 50:94-102. [PMID: 21979450 DOI: 10.1007/s10528-011-9474-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2010] [Accepted: 08/10/2011] [Indexed: 01/29/2023]
Affiliation(s)
- X Y Lan
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A&F University, 22 Xinong Road, Yangling, 712100, Shaanxi, China
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25
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McClure MC, Morsci NS, Schnabel RD, Kim JW, Yao P, Rolf MM, McKay SD, Gregg SJ, Chapple RH, Northcutt SL, Taylor JF. A genome scan for quantitative trait loci influencing carcass, post-natal growth and reproductive traits in commercial Angus cattle. Anim Genet 2011; 41:597-607. [PMID: 20477797 DOI: 10.1111/j.1365-2052.2010.02063.x] [Citation(s) in RCA: 164] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
To gain insight into the number of loci of large effect that underlie variation in cattle, a quantitative trait locus (QTL) scan for 14 economically important traits was performed in two commercial Angus populations using 390 microsatellites, 11 single nucleotide polymorphisms (SNPs) and one duplication loci. The first population comprised 1769 registered Angus bulls born between 1955 and 2003, with Expected Progeny Differences computed by the American Angus Association. The second comprised 38 half-sib families containing 1622 steers with six post-natal growth and carcass phenotypes. Linkage analysis was performed by half-sib least squares regression with gridqtl or Bayesian Markov chain Monte Carlo analysis of complex pedigrees with loki. Of the 673 detected QTL, only 118 have previously been reported, reflecting both the conservative approach to QTL reporting in the literature, and the more liberal approach taken in this study. From 33 to 71% of the genetic variance and 35 to 56% of the phenotypic variance in each trait was explained by the detected QTL. To analyse the effects of 11 SNPs and one duplication locus within candidate genes on each trait, a single marker analysis was performed by fitting an additive allele substitution model in both mapping populations. There were 53 associations detected between the SNP/duplication loci and traits with -log(10) P(nominal) ≥ 4.0, where each association explained 0.92% to 4.4% of the genetic variance and 0.01% to 1.86% of the phenotypic variance. Of these associations, only six SNP/duplication loci were located within 8 cM of a QTL peak for the trait, with two being located at the QTL peak: SST_DG156121:c.362A>G for ribeye muscle area and TG_X05380:c.422C>T for calving ease. Strong associations between several SNP/duplication loci and trait variation were obtained in the absence of any detected linked QTL. However, we reject the causality of several commercialized DNA tests, including an association between TG_X05380:c.422C>T and marbling in Angus cattle.
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Affiliation(s)
- M C McClure
- Division of Animal Sciences, University of Missouri, Columbia, MO 65211, USA
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Gill JL, Bishop SC, McCorquodale C, Williams JL, Wiener P. Associations between single nucleotide polymorphisms in multiple candidate genes and carcass and meat quality traits in a commercial Angus-cross population. Meat Sci 2010; 86:985-93. [PMID: 20826071 DOI: 10.1016/j.meatsci.2010.08.005] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2010] [Revised: 07/30/2010] [Accepted: 08/09/2010] [Indexed: 11/28/2022]
Abstract
The aim of this study was to evaluate the effects of 28 single nucleotide polymorphisms (SNP) in 10 candidate genes previously shown to be associated with quality traits in pigs and cattle. The data set comprised 28 traits recorded on a commercial population of 536 Aberdeen Angus-cross beef cattle. Among the traits, 20 were carcass and sirloin quality related, one mechanical measure of tenderness, and the remaining seven were taste panel assessed sensory traits. The candidate genes studied included growth hormone (GH) and pro-opiomelanocortin (POMC). Association analysis showed that 13 of the 28 SNPs were significantly associated with at least one of the traits. Some of these were novel (POMC and mechanical tenderness), whilst others confirmed previous results (GH and eye muscle length). Following validation in other populations and breeds, these markers could be incorporated into breeding programs to increase the rate of improvement in carcass and meat quality traits.
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Affiliation(s)
- Jennifer L Gill
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Roslin BioCentre, Roslin, Midlothian EH25 9PS, UK.
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Zhou GL, Cao Y, Li M, Zhang LC, Yu YS, Jin HG. Meat quality and carcass traits in relation to HGD-BstXI and HGD-HaeIII PCR-RFLP polymorphism in Chinese red cattle. Meat Sci 2010; 85:270-3. [PMID: 20374897 DOI: 10.1016/j.meatsci.2010.01.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2009] [Revised: 11/06/2009] [Accepted: 01/10/2010] [Indexed: 11/15/2022]
Abstract
We investigated the effect of homogentisate 1, 2 dioxygenase (HGD) gene on meat quality and carcass traits in 287 Chinese red cattle. The PCR-SSCP method was used to identify polymorphism of the HGD gene in the exon 1 and intron 1. Two polymorphisms were detected in intron 1 and two restriction sites for endonuclease HGD-BstXI and HGD-HaeIII have also been found. The HGD-BstXI genotypes showed significant effects on cooking loss, drip loss, net meat weight, carcass weight, and eye muscle area (P<0.05). The HGD-HaeIII genotypes significant affected cooking loss, muscle fibre diameter, shear force, drip loss, and carcass yield ratio (P<0.05). Moreover, we found significant effects of diplotypes on cooking loss, muscle fibre diameter, shear force, drip loss, net meat weight, carcass weight, and eye muscle area (P<0.05).
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Affiliation(s)
- G L Zhou
- College of Animal Science and Technology, Northeast Agricultural University, Harbin 150030, People's Republic of China; College of Life Science, Liaocheng University, Liaocheng 252059, People's Republic of China
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Barendse W, Bunch RJ, Harrison BE. The effect of variation at the retinoic acid receptor-related orphan receptor C gene on intramuscular fat percent and marbling score in Australian cattle1,2. J Anim Sci 2010; 88:47-51. [DOI: 10.2527/jas.2009-2178] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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29
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McElroy JA, Bryda EC, McKay SD, Schnabel RD, Taylor JF. Genetic variation at a metallothionein 2A promoter single-nucleotide polymorphism in white and black females in Midwestern United States. JOURNAL OF TOXICOLOGY AND ENVIRONMENTAL HEALTH. PART A 2010; 73:1283-7. [PMID: 20711930 DOI: 10.1080/15287394.2010.485067] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Genetic variation leading to differences in expression and regulation of metallothionein proteins may contribute to observed differences among individuals in terms of cadmium (Cd) uptake and metabolism. The aim of this study was to determine the frequency of the A and G alleles at rs28366003, which lies in the 5' promoter region of MT2A, in White and Black females in the Midwestern United States. One-milliliter saliva samples were collected from 298 White or Black adult female volunteers, and DNA was isolated from each sample using Oragene*DNA kits. Allele-specific PCR with gel visualization of amplification products was used to genotype SNP rs28366003. Of the 291 participants (Black = 142; White = 149), the average yield of DNA extracted from the saliva samples was 23.4 microg. The samples, quantitated on a spectrophotometer, achieved an average 260/280 optical density reading of 1.61. The frequency of the G allele was 1.1% for Blacks and 6.4% for Whites. Data demonstrated that the G allele is not common in both the Midwestern U.S. Black and White female population and is less frequent than that reported for an Asian population.
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Affiliation(s)
- Jane A McElroy
- Family and Community Medicine Department, University of Missouri, Columbia, Missouri 65212, USA.
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30
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Garrick DJ, Taylor JF, Fernando RL. Deregressing estimated breeding values and weighting information for genomic regression analyses. Genet Sel Evol 2009; 41:55. [PMID: 20043827 PMCID: PMC2817680 DOI: 10.1186/1297-9686-41-55] [Citation(s) in RCA: 417] [Impact Index Per Article: 27.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2009] [Accepted: 12/31/2009] [Indexed: 11/15/2022] Open
Abstract
Background Genomic prediction of breeding values involves a so-called training analysis that predicts the influence of small genomic regions by regression of observed information on marker genotypes for a given population of individuals. Available observations may take the form of individual phenotypes, repeated observations, records on close family members such as progeny, estimated breeding values (EBV) or their deregressed counterparts from genetic evaluations. The literature indicates that researchers are inconsistent in their approach to using EBV or deregressed data, and as to using the appropriate methods for weighting some data sources to account for heterogeneous variance. Methods A logical approach to using information for genomic prediction is introduced, which demonstrates the appropriate weights for analyzing observations with heterogeneous variance and explains the need for and the manner in which EBV should have parent average effects removed, be deregressed and weighted. Results An appropriate deregression for genomic regression analyses is EBV/r2 where EBV excludes parent information and r2 is the reliability of that EBV. The appropriate weights for deregressed breeding values are neither the reliability nor the prediction error variance, two alternatives that have been used in published studies, but the ratio (1 - h2)/[(c + (1 - r2)/r2)h2] where c > 0 is the fraction of genetic variance not explained by markers. Conclusions Phenotypic information on some individuals and deregressed data on others can be combined in genomic analyses using appropriate weighting.
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Affiliation(s)
- Dorian J Garrick
- Department of Animal Science, Iowa State University, Ames, IA 50011, USA.
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31
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YANG YJ, ZAN LS, WANG HB. SNPs detection of adiponectin gene and its relationship with carcass and meat quality traits in Qinchuan cattle. YI CHUAN = HEREDITAS 2009; 31:1006-12. [DOI: 10.3724/sp.j.1005.2009.01006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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32
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Simianer H, Pimentel ECG. Robust QTL fine mapping by applying a quantitative transmission disequilibrium test to the Mendelian sampling term. J Anim Breed Genet 2009; 126:432-42. [PMID: 19912417 DOI: 10.1111/j.1439-0388.2009.00812.x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In many farm animal populations, high-density single nucleotide polymorphism (SNP) genotypes are becoming available on a large scale, and routine estimation of breeding values is implemented for a multiplicity of traits. We propose to apply the basic principle of the quantitative transmission disequilibrium test (QTDT) to estimated Mendelian sampling terms. A two-step procedure is suggested, where in the first step additive breeding values are estimated with a mixed linear model and the Mendelian sampling terms are calculated from the estimated breeding values. In the second step, the QTDT is applied to these estimated Mendelian sampling terms. The resulting test is expected to yield significant results if the SNP is in sufficient linkage disequilibrium and linkage with quantitative trait loci (QTL). This principle is illustrated with a simulated data set comprising 4665 individuals genotyped for 6000 SNP and 15 true QTL. Thirteen of the fifteen QTL were significant on a genome-wide 0.1% error level. Results for the empirical power are derived from repeated samples of 1000 and 3000 genotyped individuals, respectively. General properties and potential extensions of the methodology are indicated. Owing to its computational simplicity and speed, the suggested procedure is well suited to scan whole genomes with high-density SNP coverage in samples of substantial size and for a multiplicity of different traits.
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Affiliation(s)
- H Simianer
- Department of Animal Science, Animal Breeding and Genetics Group, Georg-August-University, Goettingen, Germany.
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33
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Barendse W, Bunch RJ, Thomas MB, Harrison BE. A splice site single nucleotide polymorphism of the fatty acid binding protein 4 gene appears to be associated with intramuscular fat deposition in longissimus muscle in Australian cattle. Anim Genet 2009; 40:770-3. [PMID: 19466936 DOI: 10.1111/j.1365-2052.2009.01913.x] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Fatty acid binding protein 4 (FABP4) is a candidate gene affecting fatness traits of mammals. However, its association with fatness traits in cattle and other livestock species is not consistent from one study to another. Here, we sequenced the coding sequence of FABP4 looking for non-synonymous variants. We identified a splice site mutation between the third exon and the third intron of bovine FABP4. We genotyped this SNP, FABP4:g.2502C>G, in 1409 cattle with intramuscular fat measurements from seven breeds. The average allele frequency of the C allele was 0.66 with a range of 0.45 to 0.85. A regression on the number of G alleles shows a statistically significant effect of alpha = 0.11, P = 0.044. This appears to confirm an association between IMF and variation at FABP4, with an effect of 0.3% of the variation in our sample when using this SNP.
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Affiliation(s)
- W Barendse
- Cooperative Research Centre for Beef Genetic Technologies, CSIRO Livestock Industries, Queensland Bioscience Precinct, St Lucia 4067, Australia.
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34
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Lan X, Wei T, Zhang L, Chen H, Hu S, Lei C, Fang XT. Novel Polymorphism at the 3′ UTR of the Caprine Adiponectin Gene. Biochem Genet 2009; 47:251-6. [DOI: 10.1007/s10528-009-9223-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2008] [Accepted: 09/25/2008] [Indexed: 11/24/2022]
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Barendse W, Bunch RJ, Harrison BE. Variation at CPE but not CEBPA appears to be associated with intramuscular fat deposition in the longissimus muscle of cattle. ANIMAL PRODUCTION SCIENCE 2009. [DOI: 10.1071/ea08307] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
An important step in the localisation of quantitative trait loci is the confirmation of trait-marker associations in independent studies. In this report, we test three single nucleotide polymorphisms (SNP) of two genes for associations to intramuscular fat (IMF) measurements in cattle. We genotyped SNP of carboxypeptidase E (CPE) and ccaat/enhancer binding protein, α (CEBPA) in a sample of a total of 813 cattle of taurine, composite and indicine breeds. All three polymorphisms showed significant differences between breeds, with the widest range found in CEBPA:g.271A > C where the A allele frequency ranged from P = 0.07 in Brahman to 0.88 in Shorthorn. The taurine breeds showed high linkage disequilibrium between the pair of CPE SNP, with all four breeds showing r2 = 1.0. The Brahman and Santa Gertrudis showed r2 ≤ 0.17. Both CPE:g.445C > T and CPE:g.601C > T SNP showed significant allele substitution effects to IMF in animals of taurine ancestry, with an allele substitution effect of α = 0.22, P = 0.020 for CPE:g.445C > T, explaining 0.4% of the phenotypic variance.
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36
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Guo YK, Chen H, Zhang B, Pan CY, Zhang LZ, Zhao M, Zhang CF, Lan XY, Wang JQ. [Polymorphisms of ZAG gene with growth traits in Jiaxian red cattle]. YI CHUAN = HEREDITAS 2008; 30:1417-20. [PMID: 19073549 DOI: 10.3724/sp.j.1005.2008.01417] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The main function of ZAG gene is to enable the decomposition of fat, and reduced fat content. In this study, polymorphisms of four loci (Z1, Z2, Z3, Z4) at the coding region of the bovine ZAG gene were detected in 145 Jiaxian red cattle, and polymorphisms were found on Z1, Z3, Z4 loci. The fragments showing different SSCP patterns were sequenced, nd a total of six SNPs (C115T, A3257G, A4013G, T4027C, C4032T, and T4120C) were found. The Z3 locus of ZAG gene was at Hardy-Weinberg equilibrium, while Z1 and Z4 loci of ZAG gene were not at Hardy-Weinberg disequilibrium. The association analysis of different genotypes with some of the growth and development traits showed that the individuals with genotype AC had a larger body length, heart girth, circumference of cannon bone, body weight than the individuals with genotypes AA and AB (P<0.05 or P<0.01, respectively) in Z4 locus. It is suggest that Z4 locus may be one of the marker-assisted selection used as growth traits in Jiaxian red cattle.
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Affiliation(s)
- Yi-Kun Guo
- College of Animal Science and Technology, Northwest A & F University, Shaanxi Key Laboratory of Molecular Biology for Agriculture, Yangling, Shaanxi 712100, China.
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37
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Bian LH, Wang SZ, Wang QG, Zhang S, Wang YX, Li H. Variation at the insulin-like growth factor 1 gene and its association with body weight traits in the chicken. J Anim Breed Genet 2008; 125:265-70. [PMID: 18717967 DOI: 10.1111/j.1439-0388.2008.00739.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The insulin-like growth factor 1 (IGF1) is essential for normal embryonic and postnatal growth in mammals. In this study, a total of 342 F(2) individuals, derived from Broiler crossing to Baier layer (Northeast Agricultural University Resource Population, NEAURP), were used to investigate the associations of haplotypes in the chicken IGF1 (cIGF1) gene with body weight traits. Primers for the 5'-flanking, exon 3 and 3'-flanking regions of cIGF1 were designed according to chicken genome database. Single nucleotide polymorphisms (SNPs) between parental lines were detected by sequencing, and PCR restriction fragment length polymorphism (PCR-RFLP) and PCR single-stranded-conformation polymorphism (PCR-SSCP) methods were used to genotype the SNPs in the population. Haplotypes were constructed with the three SNPs detected. The association analysis showed that haplotypes based on three cIGF1 polymorphisms (c.-366A>C, c.528G>A and c.*1024C>T) were associated with body weight traits, suggesting that cIGF1 or a tightly linked gene had effects on body weight in the chicken.
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Affiliation(s)
- L H Bian
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, Heilongjiang, China
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38
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Garrett AJ, Rincon G, Medrano JF, Elzo MA, Silver GA, Thomas MG. Promoter region of the bovine growth hormone receptor gene: single nucleotide polymorphism discovery in cattle and association with performance in Brangus bulls. J Anim Sci 2008; 86:3315-23. [PMID: 18676722 DOI: 10.2527/jas.2008-0990] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Expression of the GH receptor (GHR) gene and its binding with GH is essential for growth and fat metabolism. A GT microsatellite exists in the promoter of bovine GHR segregating short (11 bp) and long (16 to 20 bp) allele sequences. To detect SNP and complete an association study of genotype to phenotype, we resequenced a 1,195-bp fragment of DNA including the GT microsatellite and exon 1A. Resequencing was completed in 48 familialy unrelated Holstein, Jersey, Brown Swiss, Simmental, Angus, Brahman, and Brangus cattle. Nine SNP were identified. Phylogeny analyses revealed minor distance (i.e., <5%) in DNA sequence among the 5 Bos taurus breeds; however, sequence from Brahman cattle averaged 27.4 +/- 0.07% divergence from the Bos taurus breeds, whereas divergence of Brangus was intermediate. An association study of genotype to phenotype was completed with data from growing Brangus bulls (n = 553 from 96 sires) and data from 4 of the SNP flanking the GT microsatellite. These SNP were found to be in Hardy-Weinberg equilibrium and in phase based on linkage disequilibrium analyses (r(2) = 0.84 and D'= 0.92). An A/G tag SNP was identified (ss86273136) and was located in exon 1A, which began 88 bp downstream from the GT microsatellite. Minor allele frequency of the tag SNP was greater than 10%, and Mendelian segregation was verified in 3 generation pedigrees. The A allele was derived from Brahman, and the G allele was derived from Angus. This tag SNP genotype was a significant effect in analyses of rib fat data collected with ultrasound when bulls were ~365 d of age. Specifically, bulls of the GG genotype had 6.1% more (P = 0.0204) rib fat than bulls of the AA and AG genotypes, respectively. Tag SNP (ss86273136), located in the promoter of GHR, appears to be associated with a measure of corporal fat in Bos taurus x Bos indicus composite cattle.
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Affiliation(s)
- A J Garrett
- New Mexico State University, Las Cruces 88003, USA
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39
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Zhang L, Chen H, Lan X, Zhang C, Zhang L, Zhang A, Zhang Q, Lei C, Zhang H. The novel 5bp deletion polymorphism in the promoter region of bovine ACRP30 gene. Mol Biol Rep 2008; 36:895-9. [PMID: 18446445 DOI: 10.1007/s11033-008-9260-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2007] [Accepted: 04/15/2008] [Indexed: 10/22/2022]
Abstract
ACRP30 gene was located nearby the QTL affecting the marbling, ribeye muscle area and fat thickness on the BAT1 in Angus. In this study, a 5bp deletion mutation within the bovine ACRP30 gene was firstly detected and confirmed in 991 cattle by PCR-SSCP, DNA sequencing and direct PCR amplification. The deletion mutation was appeared in Qinchuan, Nanyang, Jiaxian and Hasake, but was not found in Jinnan, Chinese Holsteins and Angus. The association of the deletion polymorphism with growth traits (including birth weight, body weight, average daily gain and body sizes in different growth periods (6/12/18/24 month-old)) was analyzed in 224 Nanyang cattle. No signification association of the deletion polymorphism with growth traits were observed (P > 0.05). The deletion was located in the promoter region and it resulted in a new putative CCAAT/enhancer binding protein-beta response element (C/EBP-RE).
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Affiliation(s)
- Liangzhi Zhang
- College of Animal Science and technology, Shaanxi Key Laboratory of Molecular Biology for Agriculture, Northwest A & F University, Yangling, Shaanx, PR China
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Sellner EM, Kim JW, McClure MC, Taylor KH, Schnabel RD, Taylor JF. Board-invited review: Applications of genomic information in livestock. J Anim Sci 2007; 85:3148-58. [PMID: 17709778 DOI: 10.2527/jas.2007-0291] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
The availability of whole genome sequences for individual species will change the landscape for livestock genomic research. Animal scientists will have access to whole-genome sequence-based technologies such as high-throughput SNP genotyping assays, gene expression profiling, methylation profiling, RNA interference, and genome resequencing that will revolutionize the scale upon which research will be conducted. These technologies will also alter the ways we think about addressing industry and scientific problems. In this review, we discuss the scientific bases for these emerging technologies and present recent highlights of their application in human, model species, and livestock as well as their potential for future applications in livestock. Additionally, we discuss strategies for their use in the genetic improvement and management of livestock. In particular, we present a strategy for the simultaneous identification of causal mutations underlying phenotypic traits in livestock and discuss issues that will arise in the application of whole genome selection for the prediction of genetic merit in livestock. We also point out that the statistical analysis that underlies the whole genome selection methodology is a sophisticated enhancement of single marker association mapping analysis to allow the entire genome to be simultaneously analyzed.
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Affiliation(s)
- E M Sellner
- Division of Animal Sciences, University of Missouri, Columbia 65211, USA
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41
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McKay SD, Schnabel RD, Murdoch BM, Aerts J, Gill CA, Gao C, Li C, Matukumalli LK, Stothard P, Wang Z, Van Tassell CP, Williams JL, Taylor JF, Moore SS. Construction of bovine whole-genome radiation hybrid and linkage maps using high-throughput genotyping. Anim Genet 2007; 38:120-5. [PMID: 17302794 PMCID: PMC2063635 DOI: 10.1111/j.1365-2052.2006.01564.x] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
High-density whole-genome maps are essential for ordering genes or markers and aid in the assembly of genome sequence. To increase the density of markers on the bovine radiation hybrid map, and hence contribute to the assembly of the bovine genome sequence, an Illumina® BeadStation was used to simultaneously type large numbers of markers on the Roslin-Cambridge 3000 rad bovine–hamster whole-genome radiation hybrid panel (WGRH3000). In five multiplex reactions, 6738 sequence tagged site (STS) markers were successfully typed on the WGRH3000 panel DNA. These STSs harboured SNPs that were developed as a result of the bovine genome sequencing initiative. Typically, the most time consuming and expensive part of creating high-density radiation hybrid (RH) maps is genotyping the markers on the RH panel with conventional approaches. Using the method described in this article, we have developed a high-density whole-genome RH map with 4690 loci and a linkage map with 2701 loci, with direct comparison to the bovine whole-genome sequence assembly (Btau_2.0) in a fraction of the time it would have taken with conventional typing and genotyping methods.
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Affiliation(s)
- S D McKay
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada.
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