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Benfica LF, Brito LF, do Bem RD, de Oliveira LF, Mulim HA, Braga LG, Cyrillo JNSG, Bonilha SFM, Mercadante MEZ. Detection and characterization of copy number variation in three differentially-selected Nellore cattle populations. Front Genet 2024; 15:1377130. [PMID: 38694873 PMCID: PMC11061390 DOI: 10.3389/fgene.2024.1377130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Accepted: 04/05/2024] [Indexed: 05/04/2024] Open
Abstract
Introduction: Nellore cattle (Bos taurus indicus) is the main beef cattle breed raised in Brazil. This breed is well adapted to tropical conditions and, more recently, has experienced intensive genetic selection for multiple performance traits. Over the past 43 years, an experimental breeding program has been developed in the Institute of Animal Science (IZ, Sertaozinho, SP, Brazil), which resulted in three differentially-selected lines known as Nellore Control (NeC), Nellore Selection (NeS), and Nellore Traditional (NeT). The primary goal of this selection experiment was to determine the response to selection for yearling weight (YW) and residual feed intake (RFI) on Nellore cattle. The main objectives of this study were to: 1) identify copy number variation (CNVs) in Nellore cattle from three selection lines; 2) identify and characterize CNV regions (CNVR) on these three lines; and 3) perform functional enrichment analyses of the CNVR identified. Results: A total of 14,914 unique CNVs and 1,884 CNVRs were identified when considering all lines as a single population. The CNVRs were non-uniformly distributed across the chromosomes of the three selection lines included in the study. The NeT line had the highest number of CNVRs (n = 1,493), followed by the NeS (n = 823) and NeC (n = 482) lines. The CNVRs covered 23,449,890 bp (0.94%), 40,175,556 bp (1.61%), and 63,212,273 bp (2.54%) of the genome of the NeC, NeS, and NeT lines, respectively. Two CNVRs were commonly identified between the three lines, and six, two, and four exclusive regions were identified for NeC, NeS, and NeT, respectively. All the exclusive regions overlap with important genes, such as SMARCD3, SLC15A1, and MAPK1. Key biological processes associated with the candidate genes were identified, including pathways related to growth and metabolism. Conclusion: This study revealed large variability in CNVs and CNVRs across three Nellore lines differentially selected for YW and RFI. Gene annotation and gene ontology analyses of the exclusive CNVRs to each line revealed specific genes and biological processes involved in the expression of growth and feed efficiency traits. These findings contribute to the understanding of the genetic mechanisms underlying the phenotypic differences among the three Nellore selection lines.
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Affiliation(s)
- Lorena F. Benfica
- Department of Animal Sciences, Purdue University, West Lafayette, IN, United States
- Department of Animal Science, Faculty of Agricultural and Veterinary Sciences, Sao Paulo State University, Jaboticabal, São Paulo, Brazil
| | - Luiz F. Brito
- Department of Animal Sciences, Purdue University, West Lafayette, IN, United States
| | - Ricardo D. do Bem
- Department of Animal Science, Faculty of Agricultural and Veterinary Sciences, Sao Paulo State University, Jaboticabal, São Paulo, Brazil
| | | | - Henrique A. Mulim
- Department of Animal Sciences, Purdue University, West Lafayette, IN, United States
| | - Larissa G. Braga
- Department of Animal Science, Faculty of Agricultural and Veterinary Sciences, Sao Paulo State University, Jaboticabal, São Paulo, Brazil
- Department of Animal Biosciences, University of Guelph, Guelph, ON, Canada
| | | | - Sarah F. M. Bonilha
- Beef Cattle Research Center, Institute of Animal Science, Sertaozinho, São Paulo, Brazil
| | - Maria Eugenia Z. Mercadante
- Department of Animal Science, Faculty of Agricultural and Veterinary Sciences, Sao Paulo State University, Jaboticabal, São Paulo, Brazil
- Beef Cattle Research Center, Institute of Animal Science, Sertaozinho, São Paulo, Brazil
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Tumino S, Bognanno M, Chessari G, Tolone M, Bordonaro S, Mangano F, Marletta D, Avondo M. Polymorphisms at Candidate Genes for Fat Content and Fatty Acids Composition: Effects on Sheep Milk Production and Fatty Acid Profile Using Two Dietary Supplementations. Animals (Basel) 2023; 13:2533. [PMID: 37570341 PMCID: PMC10417724 DOI: 10.3390/ani13152533] [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: 07/06/2023] [Revised: 08/01/2023] [Accepted: 08/04/2023] [Indexed: 08/13/2023] Open
Abstract
The nutritional value of sheep's milk and its derivatives is influenced by the lipid fraction, which is affected by diet and genetics. This study aimed to explore the genetic variations in the DGAT1 and SCD genes and assessed the impact of the DGAT1 genotype on milk quality in Valle del Belìce sheep, considering diet supplementation with carob pulp and barley grain. Among the potentially polymorphic sites, only DGAT1 g.127 C > A and SCD g.87 C > A showed variability. The DGAT1 genotype did not significantly impact milk yield and composition, except for higher urea content in the CA genotypes than in the CC ones. Carob pulp increased the milk fat content compared to barley grain. Genetic variation in DGAT1 was associated with changes in the milk fatty acid profile; specifically, the CA genotype exhibited higher levels of short-chain fatty acids and lower levels of polyunsaturated fatty acids compared to the CC genotype. Carob pulp supplementation increased saturated fatty acids and reduced unsaturated fractions, leading to milk with higher atherogenic and thrombogenic indices. No significant interaction was found between genotype and diet. This study provides insights into the genetic and dietary factors influencing sheep's milk composition. Further research is needed to understand the impact of these genetic variations on milk production and composition, as well as to determine optimal levels of carob pulp for improving fat percentage and promoting sustainable sheep breeding practices.
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Affiliation(s)
- Serena Tumino
- Dipartimento di Agricoltura, Alimentazione e Ambiente, University of Catania, 95123 Catania, Italy; (S.T.); (G.C.); (F.M.); (M.A.)
| | - Matteo Bognanno
- Dipartimento di Scienze e Tecnologie Agro-Forestali e Ambientali, University of Reggio Calabria, 89100 Reggio Calabria, Italy;
| | - Giorgio Chessari
- Dipartimento di Agricoltura, Alimentazione e Ambiente, University of Catania, 95123 Catania, Italy; (S.T.); (G.C.); (F.M.); (M.A.)
| | - Marco Tolone
- Dipartimento di Scienze Agrarie, Alimentari e Forestali, University of Palermo, 90128 Palermo, Italy;
| | - Salvatore Bordonaro
- Dipartimento di Agricoltura, Alimentazione e Ambiente, University of Catania, 95123 Catania, Italy; (S.T.); (G.C.); (F.M.); (M.A.)
| | - Fabrizio Mangano
- Dipartimento di Agricoltura, Alimentazione e Ambiente, University of Catania, 95123 Catania, Italy; (S.T.); (G.C.); (F.M.); (M.A.)
| | - Donata Marletta
- Dipartimento di Agricoltura, Alimentazione e Ambiente, University of Catania, 95123 Catania, Italy; (S.T.); (G.C.); (F.M.); (M.A.)
| | - Marcella Avondo
- Dipartimento di Agricoltura, Alimentazione e Ambiente, University of Catania, 95123 Catania, Italy; (S.T.); (G.C.); (F.M.); (M.A.)
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Li Z, He J, Yang F, Yin S, Gao Z, Chen W, Sun C, Tait RG, Bauck S, Guo W, Wu XL. A look under the hood of genomic-estimated breed compositions for brangus cattle: What have we learned? Front Genet 2023; 14:1080279. [PMID: 37056284 PMCID: PMC10086375 DOI: 10.3389/fgene.2023.1080279] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 03/14/2023] [Indexed: 04/05/2023] Open
Abstract
The Brangus cattle were developed to utilize the superior traits of Angus and Brahman cattle. Their genetic compositions are expected to be stabilized at 3/8 Brahman and 5/8 Angus. Previous studies have shown more than expected Angus lineage with Brangus cattle, and the reasons are yet to be investigated. In this study, we revisited the breed compositions for 3,605 Brangus cattle from three perspectives: genome-wise (GBC), per chromosomes (CBC), and per chromosome segments (SBC). The former (GBC) depicted an overall picture of the “mosaic” genome of the Brangus attributable to their ancestors, whereas the latter two criteria (CBC and SBC) corresponded to local ancestral contributions. The average GBC for the 3,605 Brangus cattle were 70.2% Angus and 29.8% Brahman. The K-means clustering supported the postulation of the mixture of 1/2 Ultrablack (UB) animals in Brangus. For the non-UB Brangus animals, the average GBC were estimated to be 67.4% Angus and 32.6% Brahman. The 95% confidence intervals of their overall GBC were 60.4%–73.5% Angus and 26.5%–39.6% Brahman. Possibly, genetic selection and drifting have resulted in an approximately 5% average deviation toward Angus lineage. The estimated ancestral contributions by chromosomes were heavily distributed toward Angus, with 27 chromosomes having an average Angus CBC greater than 62.5% but only two chromosomes (5 and 20) having Brahman CBC greater than 37.5%. The chromosomal regions with high Angus breed proportions were prevalent, tending to form larger blocks on most chromosomes. In contrast, chromosome segments with high Brahman breed proportion were relatively few and isolated, presenting only on seven chromosomes. Hence, genomic hitchhiking effects were strong where Angus favorable alleles resided but weak where Brahman favorable alleles were present. The functions of genes identified in the chromosomal regions with high (≥75%) Angus compositions were diverse yet may were related to growth and body development. In contrast, the genes identified in the regions with high (≥37.5%) Brahman compositions were primarily responsible for disease resistance. In conclusion, we have addressed the questions concerning the Brangus genetic make-ups. The results can help form a dynamic picture of the Brangus breed formation and the genomic reshaping.
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Affiliation(s)
- Zhi Li
- College of Animal Science and Technology, Hunan Agricultural University, Changsha, Hunan, China
| | - Jun He
- College of Animal Science and Technology, Hunan Agricultural University, Changsha, Hunan, China
- *Correspondence: Jun He, ; Xiao-Lin Wu,
| | - Fang Yang
- College of Animal Science and Technology, Hunan Agricultural University, Changsha, Hunan, China
| | - Shishu Yin
- College of Animal Science and Technology, Hunan Agricultural University, Changsha, Hunan, China
| | - Zhendong Gao
- College of Animal Science and Technology, Hunan Agricultural University, Changsha, Hunan, China
| | - Wenwu Chen
- College of Animal Science and Technology, Hunan Agricultural University, Changsha, Hunan, China
| | - Chuanyu Sun
- Biostatistics and Bioinformatics, Neogen GeneSeek, Lincoln, NE, United States
| | - Richard G. Tait
- Biostatistics and Bioinformatics, Neogen GeneSeek, Lincoln, NE, United States
| | - Stewart Bauck
- Biostatistics and Bioinformatics, Neogen GeneSeek, Lincoln, NE, United States
| | - Wei Guo
- Department of Animal and Dairy Sciences, University of Wisconsin, Madison, WI, United States
| | - Xiao-Lin Wu
- Department of Animal and Dairy Sciences, University of Wisconsin, Madison, WI, United States
- Council on Dairy Cattle Breeding, Bowie, MD, United States
- *Correspondence: Jun He, ; Xiao-Lin Wu,
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Exploring and Identifying Candidate Genes and Genomic Regions Related to Economically Important Traits in Hanwoo Cattle. Curr Issues Mol Biol 2022; 44:6075-6092. [PMID: 36547075 PMCID: PMC9777506 DOI: 10.3390/cimb44120414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 11/28/2022] [Accepted: 11/29/2022] [Indexed: 12/12/2022] Open
Abstract
The purpose of the current review was to explore and summarize different studies concerning the detection and characterization of candidate genes and genomic regions associated with economically important traits in Hanwoo beef cattle. Hanwoo cattle, the indigenous premium beef cattle of Korea, were introduced for their marbled fat, tenderness, characteristic flavor, and juiciness. To date, there has been a strong emphasis on the genetic improvement of meat quality and yields, such as backfat thickness (BFT), marbling score (MS), carcass weight (CW), eye muscle area (EMA), and yearling weight (YW), as major selection criteria in Hanwoo breeding programs. Hence, an understanding of the genetics controlling these traits along with precise knowledge of the biological mechanisms underlying the traits would increase the ability of the industry to improve cattle to better meet consumer demands. With the development of high-throughput genotyping, genomewide association studies (GWAS) have allowed the detection of chromosomal regions and candidate genes linked to phenotypes of interest. This is an effective and useful tool for accelerating the efficiency of animal breeding and selection. The GWAS results obtained from the literature review showed that most positional genes associated with carcass and growth traits in Hanwoo are located on chromosomes 6 and 14, among which LCORL, NCAPG, PPARGC1A, ABCG2, FAM110B, FABP4, DGAT1, PLAG1, and TOX are well known. In conclusion, this review study attempted to provide comprehensive information on the identified candidate genes associated with the studied traits and genes enriched in the functional terms and pathways that could serve as a valuable resource for future research in Hanwoo breeding programs.
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Khan MZ, Ma Y, Ma J, Xiao J, Liu Y, Liu S, Khan A, Khan IM, Cao Z. Association of DGAT1 With Cattle, Buffalo, Goat, and Sheep Milk and Meat Production Traits. Front Vet Sci 2021; 8:712470. [PMID: 34485439 PMCID: PMC8415568 DOI: 10.3389/fvets.2021.712470] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Accepted: 07/19/2021] [Indexed: 12/26/2022] Open
Abstract
Milk fatty acids are essential for many dairy product productions, while intramuscular fat (IMF) is associated with the quality of meat. The triacylglycerols (TAGs) are the major components of IMF and milk fat. Therefore, understanding the polymorphisms and genes linked to fat synthesis is important for animal production. Identifying quantitative trait loci (QTLs) and genes associated with milk and meat production traits has been the objective of various mapping studies in the last decade. Consistently, the QTLs on chromosomes 14, 15, and 9 have been found to be associated with milk and meat production traits in cattle, goat, and buffalo and sheep, respectively. Diacylglycerol O-acyltransferase 1 (DGAT1) gene has been reported on chromosomes 14, 15, and 9 in cattle, goat, and buffalo and sheep, respectively. Being a key role in fat metabolism and TAG synthesis, the DGAT1 has obtained considerable attention especially in animal milk production. In addition to milk production, DGAT1 has also been a subject of interest in animal meat production. Several polymorphisms have been documented in DGAT1 in various animal species including cattle, buffalo, goat, and sheep for their association with milk production traits. In addition, the DGAT1 has also been studied for their role in meat production traits in cattle, sheep, and goat. However, very limited studies have been conducted in cattle for association of DGAT1 with meat production traits in cattle. Moreover, not a single study reported the association of DGAT1 with meat production traits in buffalo; thus, further studies are warranted to fulfill this huge gap. Keeping in view the important role of DGAT1 in animal production, the current review article was designed to highlight the major development and new insights on DGAT1 effect on milk and meat production traits in cattle, buffalo, sheep, and goat. Moreover, we have also highlighted the possible future contributions of DGAT1 for the studied species.
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Affiliation(s)
- Muhammad Zahoor Khan
- State Key Laboratory of Animal Nutrition, Beijing Engineering Technology Research Center of Raw Milk Quality and Safety Control, College of Animal Science and Technology, China Agricultural University, Beijing, China
- Faculty of Veterinary and Animal Sciences, Gomal University, Dera Ismail Khan, Pakistan
| | - Yulin Ma
- State Key Laboratory of Animal Nutrition, Beijing Engineering Technology Research Center of Raw Milk Quality and Safety Control, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Jiaying Ma
- State Key Laboratory of Animal Nutrition, Beijing Engineering Technology Research Center of Raw Milk Quality and Safety Control, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Jianxin Xiao
- State Key Laboratory of Animal Nutrition, Beijing Engineering Technology Research Center of Raw Milk Quality and Safety Control, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Yue Liu
- State Key Laboratory of Animal Nutrition, Beijing Engineering Technology Research Center of Raw Milk Quality and Safety Control, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Shuai Liu
- State Key Laboratory of Animal Nutrition, Beijing Engineering Technology Research Center of Raw Milk Quality and Safety Control, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Adnan Khan
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Ibrar Muhammad Khan
- Anhui Provincial Laboratory of Local Livestock and Poultry Genetical Resource Conservation and Breeding, College of Animal Science and Technology, Anhui Agricultural University, Hefei, China
| | - Zhijun Cao
- State Key Laboratory of Animal Nutrition, Beijing Engineering Technology Research Center of Raw Milk Quality and Safety Control, College of Animal Science and Technology, China Agricultural University, Beijing, China
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Allelic and genotypic frequencies for loci associated with meat quality in Mexican Braunvieh cattle. Trop Anim Health Prod 2021; 53:307. [PMID: 33956226 DOI: 10.1007/s11250-021-02757-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Accepted: 05/02/2021] [Indexed: 10/21/2022]
Abstract
The objective was to estimate allelic and genotypic frequencies for loci associated with meat quality in a Mexican population of Braunvieh cattle. Information was obtained from 300 animals genotyped with the Genomic Profile Bovine LD chip of 30K and 50K SNPs. After the final edition, including quality control, the data contained information for 12 loci of the CAPN1, CAPN3, CAPN5, CAPN14, DGAT1, DGAT2, TG, ANK1, and MADH3 genes. Allelic and genotypic frequencies and Hardy-Weinberg equilibrium were estimated with the Cervus 3.0.7 software. The studied population markers were in Hardy-Weinberg equilibrium, except for those associated with CAPN1, DGAT1, and MADH3. Frequencies higher than those reported for other breeds were found for genotypes associated with meat softness, higher marbling score, lower quantity of saturated fatty acids, and lower shear force (CAPN1 and DGAT2). There were similarities with frequencies reported for Bos taurus breeds for the CAPN3 and TG genes. For the DGAT1 and ANK1 genes, the frequencies of the desired genotypes were low. A marker for DGAT1 and another for MADH3 were monomorphic. The results of this study are encouraging in terms of the potential of the Braunvieh population studied for breeding programs aiming to increase meat quality. The breed has strengths that could be used either by crossbreeding to generate heterozygous animals or by selection to increase frequencies of valuable alleles.
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Krovvidi S, Metta M. Evaluation of non-synonym mutation in DGAT1 K232A as a marker for milk production traits in Ongole cattle and Murrah buffalo from Southern India. Trop Anim Health Prod 2021; 53:118. [PMID: 33439326 DOI: 10.1007/s11250-021-02560-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Accepted: 01/05/2021] [Indexed: 11/25/2022]
Abstract
Various candidate genes have been reported to affect milk yield and composition in dairy cattle. A non-synonymous mutation in the DGAT1 gene, i.e., K232A was reported to have a strong association with milk yield and milk composition of Bos taurus. A study has been undertaken on 502 unrelated individuals belonging to indigenous Ongole cattle, crossbred cattle, and Murrah buffaloes from the Indian sub-continent with the objective to determine the polymorphism of the K232A locus and their association with milk yield and composition. Typing DGAT1 K232A allelic variation by PCR-RFLP using CfrI restriction enzyme revealed three genotypes in crossbred cattle. Genotype KK was more prevalent (0.60) in Jersey crossbred, whereas in Holstein Friesian crossbred it was KA genotype (0.48). In Ongole cattle and Murrah buffaloes, the locus did not exhibit polymorphism. The least-square mean of milk yields pooled over lactations across the DGAT1 variants was significantly (P < 0.05) higher among the homozygous (AA) genotypes, both in Jersey crossbred and HF crossbred cattle after adjusting for the effects of farm, parity, and season. The fat, SNF, and protein content values of AA genotypes were less than the KK genotypes in both the genetic groups (P > 0.05). The fixation of the DGAT1K allele at the locus in Bos indicus cattle and Bubalus bubalis in the present study did not support its use as a reliable universal marker for milk production and composition traits.
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Affiliation(s)
- Sudhakar Krovvidi
- Department of Animal Genetics and Breeding, NTR College of Veterinary Science (Sri Venkateswara Veterinary University), Gannavaram, Andhra Pradesh, 521 102, India.
| | - Muralidhar Metta
- Department of Animal Genetics and Breeding, NTR College of Veterinary Science (Sri Venkateswara Veterinary University), Gannavaram, Andhra Pradesh, 521 102, India
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PATHAK PRAJWALITA, MUKHERJEE ANUPAMA, NAYAK VIVEKKUMAR, KUMAR SUCHIT, MUMTAZ SHABAHAT, MUMTAZ SHABAHAT, YADAV ALOKKUMAR. Association of genetic polymorphism in leptin gene with growth, reproduction and production traits in Sahiwal cows. THE INDIAN JOURNAL OF ANIMAL SCIENCES 2021. [DOI: 10.56093/ijans.v90i8.109291] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The present study explored the association between single nucleotide polymorphisms (SNPs) in leptin gene with various economic traits (body weight at different age, first lactation reproduction and production traits) in Sahiwal cows. PCR-RFLP of 522 bp fragment comprising partial intron 2 and exon 3 of leptin gene, carried out using BsaAI restriction endonuclease, revealed three genotypes (GG, AG and AA) at position G93263736A in chromosome 4 with genotypic frequencies of 0.39, 0.52 and 0.09 respectively. The allele frequencies were 0.65 for the G allele and 0.35 for the A allele. General Linear Model (GLM) analysis revealed significant association of SNP G93263736A with growth and first lactation production traits. The present study supports that SNP in leptin gene could be used as an aid to selection for improving different economic traits in Sahiwal cows.
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Paim TDP, Hay EHA, Wilson C, Thomas MG, Kuehn LA, Paiva SR, McManus C, Blackburn H. Genomic Breed Composition of Selection Signatures in Brangus Beef Cattle. Front Genet 2020; 11:710. [PMID: 32754198 PMCID: PMC7365941 DOI: 10.3389/fgene.2020.00710] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Accepted: 06/11/2020] [Indexed: 12/13/2022] Open
Abstract
Cattle breeding routinely uses crossbreeding between subspecies (Bos taurus taurus and Bos taurus indicus) to form composite breeds, such as Brangus. These composite breeds provide an opportunity to identify recent selection signatures formed in the new population and evaluate the genomic composition of these regions of the genome. Using high-density genotyping, we first identified runs of homozygosity (ROH) and calculated genomic inbreeding. Then, we evaluated the genomic composition of the regions identified as selected (selective sweeps) using a chromosome painting approach. The genomic inbreeding increased at approximately 1% per generation after composite breed formation, showing the need of inbreeding control even in composite breeds. Three selected regions in Brangus were also identified as Angus selection signatures. Two regions (chromosomes 14 and 21) were identified as signatures of selection in Brangus and both founder breeds. Five of the 10 homozygous regions in Brangus were predominantly Angus in origin (probability >80%), and the other five regions had a mixed origin but always with Brahman contributing less than 50%. Therefore, genetic events, such as drift, selection, and complementarity, are likely shaping the genetic composition of founder breeds in specific genomic regions. Such findings highlight a variety of opportunities to better control the selection process and explore heterosis and complementarity at the genomic level in composite breeds.
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Affiliation(s)
- Tiago do Prado Paim
- Instituto Federal de Educação, Ciência e Tecnologia Goiano, Iporá, Brazil
- Universidade de Brasília, Brasília, Brazil
| | - El Hamidi A. Hay
- Fort Keogh Livestock and Range Research Laboratory, Agricultural Research Service, United States Department of Agriculture, Miles City, MO, United States
| | - Carrie Wilson
- National Animal Germplasm Program, National Laboratory for Genetic Resources Preservation, Agricultural Research Service, United States Department of Agriculture, Fort Collins, CO, United States
| | - Milt G. Thomas
- Department of Animal Sciences, Colorado State University, Fort Collins, CO, United States
| | - Larry A. Kuehn
- United States Meat Animal Research Center, Agricultural Research Service, United States Department of Agriculture, Clay Center, NE, United States
| | - Samuel R. Paiva
- Embrapa Recursos Genéticos e Biotecnologia, Brasília, Brazil
| | | | - Harvey Blackburn
- National Animal Germplasm Program, National Laboratory for Genetic Resources Preservation, Agricultural Research Service, United States Department of Agriculture, Fort Collins, CO, United States
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Akhmetov TM, Safina NY, Alimov AM, Varlamova MI. Genetic parameters of milk productivity for three lactations of Holstein cattle with different genotypes of LEP gene. BIO WEB OF CONFERENCES 2020. [DOI: 10.1051/bioconf/20202700061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The research presents the findings of DNA testing of allelic polymorphism by the AC-PCR method of the LEP gene. The research was conducted among 172 Holstein cows at Integrated Agricultural Production Centre “Stud farm named after Lenin” in Atninsky district of the Republic of Tatarstan in 2017–2018. All genotypes of the LEP gene were identified through the research. Associations of the leptin gene polymorphism with dynamics of milk production during three lactations of Holstein cows were established. The best indicators for all three lactations were found in a group of animals with the TT genotype of the LEP gene. These individuals are characterized by increased milk yield, a high yield index, and tend to increase the average daily milk yield during three lactations. These individuals are characterized by increased milk yield, a high milk yield index, and tend to increase the average daily milk yield during three lactations.
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Association of Twelve Candidate Gene Polymorphisms with the Intramuscular Fat Content and Average Backfat Thickness of Chinese Suhuai Pigs. Animals (Basel) 2019; 9:ani9110858. [PMID: 31652864 PMCID: PMC6912197 DOI: 10.3390/ani9110858] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Revised: 10/18/2019] [Accepted: 10/21/2019] [Indexed: 12/16/2022] Open
Abstract
Simple Summary Appropriate intramuscular fat content (IFC) is the goal of consumers and the direction that breeders must pursue. However, it is difficult to improve the IFC but not average backfat thickness (ABT) by traditional breeding methods, and pigs must be slaughtered to accurately measure IFC. Marker-assisted selection (MAS) provides an economic and efficient method to improve the IFC in pigs. Our research indicated that the FABP3 (rs1110770079) single nucleotide polymorphism (SNP) could be a candidate gene associated with IFC (but not ABT), and IFC could be improved by selecting the individuals with a favorable genotype (GG) of FABP3 (rs1110770079) SNP for pig breeding. Abstract The present study aimed to identify the molecular markers for genes that influence intramuscular fat content (IFC), but not average backfat thickness (ABT). A total of 330 Suhuai pigs were slaughtered, and measurements of IFC and ABT were obtained. Phenotypic and genetic correlations between IFC and ABT were calculated. Thirteen single nucleotide polymorphisms (SNPs) among 12 candidate genes for IFC were analyzed, including FABP3, LIPE, IGF1, IGF2, LEP, LEPR, MC4R, PHKG1, RETN, RYR1, SCD, and UBE3C. Associations of the evaluated SNPs with IFCIFC and ABT were performed. Our results showed that the means of IFC and ABT were 1.99 ± 0.03 % and 26.68 ± 0.28 mm, respectively. The coefficients of variation (CVs) of IFC and ABT were 31.21% and 19.36%, respectively. The phenotypic and genetic correlations between IFC and ABT were moderate. Only the FABP3 (rs1110770079) was associated with IFC (p < 0.05) but not with ABT. Besides, there was a tendency for associations of RYR1 (rs344435545) and SCD (rs80912566) with IFC (p < 0.1). Our results indicated that the FABP3 (rs1110770079) SNP could be used as a marker to improve IFC without changing ABT in the Suhuai pig breeding system.
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Migdal L, Koziol K, Palka S, Migdal W, Zabek T, Otwinowska-Mindur A, Migdal A, Kmiecik M, Maj D, Bieniek J. Mutations in Leptin (LEP) Gene Are Associated with Carcass and Meat Quality Traits in Crossbreed Rabbits. Anim Biotechnol 2017; 29:153-159. [DOI: 10.1080/10495398.2017.1347881] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Lukasz Migdal
- Department of Genetics and Animal Breeding, Faculty of Animal Sciences, University of Agriculture in Krakow, Krakow, Poland
| | - Konrad Koziol
- Department of Genetics and Animal Breeding, Faculty of Animal Sciences, University of Agriculture in Krakow, Krakow, Poland
| | - Sylwia Palka
- Department of Genetics and Animal Breeding, Faculty of Animal Sciences, University of Agriculture in Krakow, Krakow, Poland
| | - Wladyslaw Migdal
- Department of Animal Product Technology, Faculty of Food Technology, University of Agriculture in Krakow, Krakow, Poland
| | - Tomasz Zabek
- Department of Genomics and Animal Molecular Biology, National Research Institute of Animal Production Poland
| | - Agnieszka Otwinowska-Mindur
- Department of Genetics and Animal Breeding, Faculty of Animal Sciences, University of Agriculture in Krakow, Krakow, Poland
| | - Anna Migdal
- Institute of Veterinary Sciences, Faculty of Animal Sciences, University of Agriculture in Krakow, Krakow, Poland
| | - Michal Kmiecik
- Department of Genetics and Animal Breeding, Faculty of Animal Sciences, University of Agriculture in Krakow, Krakow, Poland
| | - Dorota Maj
- Department of Genetics and Animal Breeding, Faculty of Animal Sciences, University of Agriculture in Krakow, Krakow, Poland
| | - Jozef Bieniek
- Department of Genetics and Animal Breeding, Faculty of Animal Sciences, University of Agriculture in Krakow, Krakow, Poland
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Wang C, Zhang H, Niu L, Guo J, Jia X, Wang L, Li L, Zhang H, Zhong T. The novel SNPs of leptin gene and their associations with growth traits in Chinese Nanjiang Yellow goat. Gene 2015; 572:35-41. [PMID: 26142105 DOI: 10.1016/j.gene.2015.06.073] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2014] [Revised: 06/08/2015] [Accepted: 06/27/2015] [Indexed: 01/09/2023]
Abstract
The leptin (LEP) gene encodes a protein that greatly affects the regulation of body weight, energy balance, and food intake in mammals. The objective of the present work was to identify genetic variants of the caprine LEP gene in 411 individuals from five Chinese goat breeds. Six novel single nucleotide polymorphisms (SNPs) (g.117T > C, g.1642G > A, g.2883G > A, g.3053T > C, g.3190G > A, and g.3314T > C) were detected using DNA sequencing. A chi-squared (χ(2)) test showed that all of the LEP SNPs were in Hardy-Weinberg equilibrium in the studied population (P > 0.05). Six common haplotypes were identified in the five goat populations, with frequencies ranging from 0.083 to 0.244. The r(2) linkage disequilibrium plot of the LEP SNPs indicated linkage disequilibrium only in the cultured breeds (NJ and JY). Statistical analysis revealed that all of the six SNPs of the LEP gene were associated with growth traits. The individuals with the GG genotype at g.1642G>A and g.3190G > A loci showed higher birth weight (2.38 ± 0.03, 2.43 ± 0.05) and weight at 2 months of age (10.59 ± 0.16, 10.71 ± 0.26) than the A-bearing genotypes (AA or GA, P < 0.05). Our findings indicate that polymorphisms of the caprine LEP gene might be important genetic factors influencing growth traits, and these genetic markers may be useful for future marker-assisted selection programs in goat breeding and production.
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Affiliation(s)
- Cen Wang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Hao Zhang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Lili Niu
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Jiazhong Guo
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Xianbo Jia
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Linjie Wang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Li Li
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Hongping Zhang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Tao Zhong
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China.
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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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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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de Oliveira JA, da Cunha CM, Crispim BDA, Seno LDO, Fernandes ARM, Nogueira GDP, Grisolia AB. Association of the leptin gene with carcass characteristics in Nellore cattle. Anim Biotechnol 2013; 24:229-42. [PMID: 23777351 DOI: 10.1080/10495398.2013.770008] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Advances in DNA technology have created biotechnological tools that can be used in animal selection and new strategies for increasing herd productivity and quality. The objective of the present work was to associate the genotypes of leptin gene exon 2 polymorphisms with productive traits in Nellore cattle. Blood was collected from Nellore males and PCR-RFLP reactions were performed with the restriction enzymes Cla I and Kpn 2I. The gene frequencies resulting from digestion by Cla I were 0.60 and 0.40 for allele A and T, respectively; the genotypic frequencies were AA = 0.20 and AT = 0.80. The gene frequencies from digestion by Kpn 2I were 0.81 for allele C and 0.194 for allele T; the genotypic frequencies were CC = 0.62 and CT = 0.38. The populations in both cases were not in Hardy-Weinberg equilibrium (p > 0.05), and the TT genotype was not found. Significant associations were noted between leptin gene exon 2 polymorphisms and five productive traits in Nellore cattle: carcass fat distribution, the intensity of red muscle coloration, pH, marbling, and post-slaughter fat thickness.
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Affiliation(s)
- Joyce Azambuja de Oliveira
- Faculdade de Ciências Biológicas e Ambientais, Universidade Federal da Grande Dourados, Dourados - MS, Brasil.
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Zetouni L, de Camargo GMF, da Silva Fonseca PD, Gil FMM, Lugo NAH, Aspilcueta-Borquis RR, Cervini M, Tonhati H. Effects of a single nucleotide polymorphism in the leptin gene on the productive traits of dairy buffaloes (Bubalus bubalis). Mol Biol Rep 2013; 40:5159-63. [PMID: 23661024 DOI: 10.1007/s11033-013-2618-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2012] [Accepted: 04/30/2013] [Indexed: 12/31/2022]
Abstract
The gene responsible for coding the leptin hormone has been associated with productive and reproductive traits in cattle. In dairy cattle, different polymorphisms found in the leptin gene have been associated with several traits of economic interest, such as energy balance, milk yield and composition, live weight, fertility and dry matter consumption. The aim of this study was to detect genetic variability in the leptin gene of buffaloes and to test possible associations with milk yield, fat and protein percentages, age at first calving and first calving interval. Three genotypes (AA, AG and GG) were identified by polymerase chain reaction-restriction fragment length polymorphism, which presented genotypic frequencies of 0.30, 0.54 and 0.16, respectively. The allele frequencies were 0.57 for the A allele and 0.43 for the G allele. No significant effects were found in the present study, but there is an indicative that leptin gene affects lipid metabolism.
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Affiliation(s)
- Larissa Zetouni
- Animal Sciences Departament, São Paulo State University, Campus Jaboticabal, Via de Acesso Prof. Paulo Donato Castellane, s/n-CEP, Jaboticabal, SP, 14884-900, Brazil.
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Effects of DGAT1 gene on meat and carcass fatness quality in Chinese commercial cattle. Mol Biol Rep 2012; 40:1947-54. [PMID: 23143182 DOI: 10.1007/s11033-012-2251-2] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2012] [Accepted: 10/10/2012] [Indexed: 02/02/2023]
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da Silva RCG, Ferraz JBS, Meirelles FV, Eler JP, Balieiro JCC, Cucco DC, Mattos EC, Rezende FM, Silva SL. Association of single nucleotide polymorphisms in the bovine leptin and leptin receptor genes with growth and ultrasound carcass traits in Nellore cattle. GENETICS AND MOLECULAR RESEARCH 2012; 11:3721-8. [PMID: 22930433 DOI: 10.4238/2012.august.17.10] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Given the important role of leptin in metabolism, we looked for a possible association of leptin and leptin receptor polymorphisms with carcass and growth traits in Nellore cattle. We examined associations of leptin and leptin receptor SNPs with ultrasound carcass (longissimus dorsi muscle area (ribeye area), backfat thickness and rump fat thickness and growth traits (weaning weight adjusted to 210 days of age, yearling weight adjusted to 550 days of age, weight gain of weaning to yearling and scrotal circumference adjusted to 550 days of age) of 2162 Bos primigenius indicus (Nellore) animals. Allele and genotypic frequencies were calculated for each marker. Allele substitution, additive and dominance effects of the polymorphisms were also evaluated. Some alleles of the molecular markers had low frequencies, lower than 1%, in the sample analyzed, although the same polymorphisms described for B. p. taurus cattle were found. Due to very low allelic frequencies, the E2JW, A59V and UASMS2 markers were not included in the analysis, because they were almost fixed. E2FB was found to be significantly associated with weight gain, ribeye area and backfat thickness. The promoter region markers, C963T and UASMS1, were also found to be significantly associated with ribeye area. T945M was significantly associated with weight gain. We conclude that the leptin and receptor gene markers would be useful for marker-assisted selection.
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Martins da Silva A, Rios A, Ramos E, Lôbo R, Oliveira H, de Freitas M. Association between IGF2 and CYP21 gene polymorphisms and characteristics of economic interest in Nellore cattle. GENETICS AND MOLECULAR RESEARCH 2011; 10:2140-7. [DOI: 10.4238/vol10-3gmr1184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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