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Asselstine V, Medrano JF, Muniz MMM, Mallard BA, Karrow NA, Cánovas A. Novel lncRNA regulatory elements in milk somatic cells of Holstein dairy cows associated with mastitis. Commun Biol 2024; 7:98. [PMID: 38225372 PMCID: PMC10789785 DOI: 10.1038/s42003-024-05764-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Accepted: 01/01/2024] [Indexed: 01/17/2024] Open
Abstract
Despite regulatory elements such as long non - coding RNAs representing most of the transcriptome, the functional understanding of long non - coding RNAs in relation to major health conditions including bovine mastitis is limited. This study examined the milk somatic cell transcriptome from udder quarters of 6 Holstein dairy cows to identify differentially expressed long non - coding RNAs using RNA - Sequencing. Ninety - four differentially expressed long non - coding RNAs are identified, 5 of which are previously annotated for gene name and length, 11 are annotated for gene name and 78 are novel, having no gene name or length previously annotated. Significant inflammatory response and regulation of immune response pathways (false discovery rate < 0.05) are associated with the differentially expressed long non - coding RNAs. QTL annotation analysis revealed 31 QTL previously annotated in the genomic regions of the 94 differentially expressed long non - coding RNAs, and the majority are associated with milk traits. This research provides a better understanding of long non - coding RNAs regulatory elements in milk somatic cells, which may enhance current breeding strategies for more adaptable or high mastitis resistant cattle.
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Affiliation(s)
- Victoria Asselstine
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, N1G 2W1, Guelph, ON, Canada
| | - Juan F Medrano
- Department of Animal Science, University of California-Davis, 95616, Davis, CA, USA
| | - Malane M M Muniz
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, N1G 2W1, Guelph, ON, Canada
| | - Bonnie A Mallard
- Department of Pathobiology, Ontario Veterinary College, University of Guelph, N1G 2W1, Guelph, ON, Canada
| | - Niel A Karrow
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, N1G 2W1, Guelph, ON, Canada
| | - Angela Cánovas
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, N1G 2W1, Guelph, ON, Canada.
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Intra- and Interspecies RNA-Seq Based Variants in the Lactation Process of Ruminants. Animals (Basel) 2022; 12:ani12243592. [PMID: 36552512 PMCID: PMC9774614 DOI: 10.3390/ani12243592] [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: 09/18/2022] [Revised: 11/07/2022] [Accepted: 12/16/2022] [Indexed: 12/23/2022] Open
Abstract
The RNA-Seq data provides new opportunities for the detection of transcriptome variants' single nucleotide polymorphisms (SNPs) in various species and tissues. Herein, milk samples from two sheep breeds and two cow breeds were utilized to characterize the genetic variation in the coding regions in three stages (before-peak (BP), peak (P), and after-peak (AP)) of the lactation process. In sheep breeds Assaf and Churra, 100,462 and 97,768, 65,996 and 62,161, and 78,656 and 39,245 variants were observed for BP, P, and AP lactation stages, respectively. The number of specific variants was 59,798 and 76,419, 11,483 and 49,210, and 104,033 and 320,817 in cow breeds Jersy and Kashmiri, respectively, for BP, P, and AP stages. Via the transcriptome analysis of variation in regions containing QTL for fat, protein percentages, and milk yield, we detected a number of pathways and genes harboring mutations that could influence milk production attributes. Many SNPs detected here can be regarded as appropriate markers for custom SNP arrays or genotyping platforms to conduct association analyses among commercial populations. The results of this study offer new insights into milk production genetic mechanisms in cow and sheep breeds, which can contribute to designing suitable breeding systems for optimal milk production.
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Cieślińska A, Fiedorowicz E, Rozmus D, Sienkiewicz-Szłapka E, Jarmołowska B, Kamiński S. Does a Little Difference Make a Big Difference? Bovine β-Casein A1 and A2 Variants and Human Health-An Update. Int J Mol Sci 2022; 23:15637. [PMID: 36555278 PMCID: PMC9779325 DOI: 10.3390/ijms232415637] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2022] [Revised: 12/01/2022] [Accepted: 12/05/2022] [Indexed: 12/14/2022] Open
Abstract
For over 20 years, bovine beta-casein has been a subject of increasing scientific interest because its genetic A1 variant during gastrointestinal digestion releases opioid-like peptide β-casomorphin-7 (β-CM-7). Since β-CM-7 is involved in the dysregulation of many physiological processes, there is a growing discussion of whether the consumption of the β-casein A1 variant has an influence on human health. In the last decade, the number of papers dealing with this problem has substantially increased. The newest clinical studies on humans showed a negative effect of variant A1 on serum glutathione level, digestive well-being, cognitive performance score in children, and mood score in women. Scientific reports in this field can affect the policies of dairy cattle breeders and the milk industry, leading to the elimination of allele A1 in dairy cattle populations and promoting milk products based on milk from cows with the A2A2 genotype. More scientific proof, especially in well-designed clinical studies, is necessary to determine whether a little difference in the β-casein amino acid sequence negatively affects the health of milk consumers.
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Affiliation(s)
- Anna Cieślińska
- Department of Biochemistry, Faculty of Biology and Biotechnology, University of Warmia and Mazury, 10-719 Olsztyn, Poland
| | - Ewa Fiedorowicz
- Department of Biochemistry, Faculty of Biology and Biotechnology, University of Warmia and Mazury, 10-719 Olsztyn, Poland
| | - Dominika Rozmus
- Department of Biochemistry, Faculty of Biology and Biotechnology, University of Warmia and Mazury, 10-719 Olsztyn, Poland
| | - Edyta Sienkiewicz-Szłapka
- Department of Biochemistry, Faculty of Biology and Biotechnology, University of Warmia and Mazury, 10-719 Olsztyn, Poland
| | - Beata Jarmołowska
- Department of Biochemistry, Faculty of Biology and Biotechnology, University of Warmia and Mazury, 10-719 Olsztyn, Poland
| | - Stanisław Kamiński
- Department of Animal Genetics, University of Warmia and Mazury, 10-719 Olsztyn, Poland
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Rahmatalla SA, Arends D, Brockmann GA. Review: Genetic and protein variants of milk caseins in goats. Front Genet 2022; 13:995349. [PMID: 36568379 PMCID: PMC9768343 DOI: 10.3389/fgene.2022.995349] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Accepted: 10/03/2022] [Indexed: 12/12/2022] Open
Abstract
The milk casein genes in goats, are highly polymorphic genes with numerous synonymous and non-synonymous mutations. So far, 20 protein variants have been reported in goats for alpha-S1-casein, eight for beta-casein, 14 for alpha-S2-casein, and 24 for kappa-casein. This review provides a comprehensive overview on identified milk casein protein variants in goat and non-coding DNA sequence variants with some affecting the expression of the casein genes. The high frequency of some casein protein variants in different goat breeds and geographical regions might reflect specific breeding goals with respect to milk processing characteristics, properties for human nutrition and health, or adaptation to the environment. Because protein names, alongside the discovery of protein variants, go through a historical process, we linked old protein names with new ones that reveal more genetic variability. The haplotypes across the cluster of the four genetically linked casein genes are recommended as a valuable genetic tool for discrimination between breeds, managing genetic diversity within and between goat populations, and breeding strategies. The enormous variation in the casein proteins and genes is crucial for producing milk and dairy products with different properties for human health and nutrition, and for genetic improvement depending on local breeding goals.
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Affiliation(s)
- Siham A. Rahmatalla
- Animal Breeding and Molecular Genetics, Albrecht Daniel Thaer-Institute of Agricultural and Horticultural Sciences, Humboldt University of Berlin, Berlin, Germany,Department of Dairy Production, Faculty of Animal Production, University of Khartoum, Khartoum North, Sudan,*Correspondence: Siham A. Rahmatalla, ; Gudrun A. Brockmann,
| | - Danny Arends
- Animal Breeding and Molecular Genetics, Albrecht Daniel Thaer-Institute of Agricultural and Horticultural Sciences, Humboldt University of Berlin, Berlin, Germany,Department of Applied Sciences, Northumbria University, Newcastle upon Tyne, United Kingdom
| | - Gudrun A. Brockmann
- Animal Breeding and Molecular Genetics, Albrecht Daniel Thaer-Institute of Agricultural and Horticultural Sciences, Humboldt University of Berlin, Berlin, Germany,*Correspondence: Siham A. Rahmatalla, ; Gudrun A. Brockmann,
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Novel nitrogen mustard-artemisinin hybrids with potent anti-leukemia action through DNA damage and activation of GPx. Eur J Med Chem 2022; 244:114783. [DOI: 10.1016/j.ejmech.2022.114783] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2022] [Revised: 09/12/2022] [Accepted: 09/15/2022] [Indexed: 11/22/2022]
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Buzás H, Székelyhidi R, Szafner G, Szabó K, Süle J, Bukovics S, Kovács AJ. Developed rapid and simple RP-HPLC method for simultaneous separation and quantification of bovine milk protein fractions and their genetic variants. Anal Biochem 2022; 658:114939. [DOI: 10.1016/j.ab.2022.114939] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Revised: 09/23/2022] [Accepted: 09/29/2022] [Indexed: 11/01/2022]
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Atashi H, Bastin C, Wilmot H, Vanderick S, Hubin X, Gengler N. Genome-wide association study for selected cheese-making properties in Dual-Purpose Belgian Blue cows. J Dairy Sci 2022; 105:8972-8988. [PMID: 36175238 DOI: 10.3168/jds.2022-21780] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Accepted: 06/21/2022] [Indexed: 01/05/2023]
Abstract
This study aimed to estimate genetic parameters and identify genomic region(s) associated with selected cheese-making properties (CMP) in Dual-Purpose Belgian Blue (DPBB) cows. Edited data were 46,301 test-day records of milk yield, fat percentage, protein percentage, casein percentage, milk calcium content (CC), coagulation time (CT), curd firmness after 30 min from rennet addition (a30), and milk titratable acidity (MTA) collected from 2014 to 2020 on 4,077 first-parity (26,027 test-day records), and 3,258 second-parity DPBB cows (20,274 test-day records) distributed in 124 herds in the Walloon Region of Belgium. Data of 28,266 SNP, located on 29 Bos taurus autosomes (BTA) of 1,699 animals were used. Random regression test-day models were used to estimate genetic parameters through the Bayesian Gibbs sampling method. The SNP solutions were estimated using a single-step genomic BLUP approach. The proportion of the total additive genetic variance explained by windows of 25 consecutive SNPs (with an average size of ∼2 Mb) was calculated, and regions accounting for at least 1.0% of the total additive genetic variance were used to search for candidate genes. Heritability estimates for the included CMP ranged from 0.19 (CC) to 0.50 (MTA), and 0.24 (CC) to 0.41 (MTA) in the first and second parity, respectively. The genetic correlation estimated between CT and a30 varied from -0.61 to -0.41 and from -0.55 to -0.38 in the first and second lactations, respectively. Negative genetic correlations were found between CT and milk yield and composition, while those estimated between curd firmness and milk composition were positive. Genome-wide association analyses results identified 4 genomic regions (BTA1, BTA3, BTA7, and BTA11) associated with the considered CMP. The identified genomic regions showed contrasting results between parities and among the different stages of each parity. It suggests that different sets of candidate genes underlie the phenotypic expression of the considered CMP between parities and lactation stages of each parity. The findings of this study can be used for future implementation and use of genomic evaluation to improve the cheese-making traits in DPBB cows.
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Affiliation(s)
- H Atashi
- TERRA Teaching and Research Center, Gembloux Agro-Bio Tech, University of Liège, 5030 Gembloux, Belgium; Department of Animal Science, Shiraz University, 71441-65186 Shiraz, Iran.
| | - C Bastin
- Walloon Breeders Association, 5590 Ciney, Belgium
| | - H Wilmot
- TERRA Teaching and Research Center, Gembloux Agro-Bio Tech, University of Liège, 5030 Gembloux, Belgium; National Fund for Scientific Research (FRS-FNRS), Rue d'Egmont 5, B-1000 Brussels, Belgium
| | - S Vanderick
- TERRA Teaching and Research Center, Gembloux Agro-Bio Tech, University of Liège, 5030 Gembloux, Belgium
| | - X Hubin
- Walloon Breeders Association, 5590 Ciney, Belgium
| | - N Gengler
- TERRA Teaching and Research Center, Gembloux Agro-Bio Tech, University of Liège, 5030 Gembloux, Belgium
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Kis J, Rózsa L, Husvéth F, Zsolnai A, Anton I. Role of genes related to performance and reproduction of Thoroughbreds in training and breeding - A review. Acta Vet Hung 2021; 69:315-323. [PMID: 34739392 DOI: 10.1556/004.2021.00045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 10/01/2021] [Indexed: 11/19/2022]
Abstract
Thoroughbreds have been selected for speed and stamina since the 1700s. This selection resulted in structural and functional system-wide adaptations that enhanced physiological characteristics for outstanding speed of 61-71 kph (38-44 mph) between 1,000 and 3,200 m (5 furlongs - 2 miles). At present, horseracing is still an economically important industrial sector, therefore intensive research is underway to explore genes that allow the utilisation of genetic abilities and are significant in breeding and training. This study aims to provide an overview of genetic research and its applicability related to Thoroughbreds.
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Affiliation(s)
- Judit Kis
- 1Department of Animal Breeding, Institute of Animal Science, Hungarian University of Agriculture and Life Sciences, Kaposvár Campus, Guba Sándor u. 40, H-7400 Kaposvár, Hungary
| | - László Rózsa
- 1Department of Animal Breeding, Institute of Animal Science, Hungarian University of Agriculture and Life Sciences, Kaposvár Campus, Guba Sándor u. 40, H-7400 Kaposvár, Hungary
| | - Ferenc Husvéth
- 2Department of Animal Breeding, Institute of Animal Science, Hungarian University of Agriculture and Life Sciences, Georgikon Campus, Hungary
| | - Attila Zsolnai
- 1Department of Animal Breeding, Institute of Animal Science, Hungarian University of Agriculture and Life Sciences, Kaposvár Campus, Guba Sándor u. 40, H-7400 Kaposvár, Hungary
| | - István Anton
- 1Department of Animal Breeding, Institute of Animal Science, Hungarian University of Agriculture and Life Sciences, Kaposvár Campus, Guba Sándor u. 40, H-7400 Kaposvár, Hungary
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Anggraeni A, Syifa L, Kurnia Sari O, Baso Lompengeng Ishak A, Sumantri C. Polymorphism of CSN1S1 (g.12164G>A) and CSN2 (g.8913C>A) genes in pure and cross dairy goats. BIO WEB OF CONFERENCES 2021. [DOI: 10.1051/bioconf/20213302001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Casein genes directly control milk protein of animals. CSN1S1 (αS1-Casein) and CSN2 (β-Casein) genes influence on milk protein fractions. Genetic polymorphisms of CSN1S1 gene at g.12164G>A locus and CSN2 gene at g.8913C>A locus were identified by PCR-RFLP technique. Animal samples were pure dairy goats providing PE (5 hds.), Saanen (8 hds.) and their crosses providing Sapera (50% Saanen, 50% PE) (51 hds.) and SaanPE (75% Saanen, 25% PE) (3 hds.) from IRIAP dairy goat station. Allele frequency, genotype frequency, heterozygosity value, and Hardy-Weinberg (H-W) equilibrium value were analyzed by Popgen32 program. CSN1S1_g.12164G>A locus resulted in two alleles, i.e. G allele (192 bp, 145 bp, and 101 bp) and A allele (337 bp and 101 bp). The G allele from the highest frequenciest was successively Saanen (0.625), Sapera (0.578), PE (0.400), and SaanPE (0.333). Most dairy goats were heterozygote (Ho>He) and in H-W equilibrium (q2 count < q2P0.05). Whereas CSN2_g.8913C>A locus was monomorphic for possesing only C allele (233 bp and 162 bp), without A allele (416 bp). The existent g.12164G>A SNP of the CSN1S1 gene of could be a potencial molecular selection marker of milk protein content in dairy goat.
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α-Lactalbumin, Amazing Calcium-Binding Protein. Biomolecules 2020; 10:biom10091210. [PMID: 32825311 PMCID: PMC7565966 DOI: 10.3390/biom10091210] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 08/14/2020] [Accepted: 08/17/2020] [Indexed: 02/06/2023] Open
Abstract
α-Lactalbumin (α-LA) is a small (Mr 14,200), acidic (pI 4–5), Ca2+-binding protein. α-LA is a regulatory component of lactose synthase enzyme system functioning in the lactating mammary gland. The protein possesses a single strong Ca2+-binding site, which can also bind Mg2+, Mn2+, Na+, K+, and some other metal cations. It contains several distinct Zn2+-binding sites. Physical properties of α-LA strongly depend on the occupation of its metal binding sites by metal ions. In the absence of bound metal ions, α-LA is in the molten globule-like state. The binding of metal ions, and especially of Ca2+, increases stability of α-LA against the action of heat, various denaturing agents and proteases, while the binding of Zn2+ to the Ca2+-loaded protein decreases its stability and causes its aggregation. At pH 2, the protein is in the classical molten globule state. α-LA can associate with membranes at neutral or slightly acidic pH at physiological temperatures. Depending on external conditions, α-LA can form amyloid fibrils, amorphous aggregates, nanoparticles, and nanotubes. Some of these aggregated states of α-LA can be used in practical applications such as drug delivery to tissues and organs. α-LA and some of its fragments possess bactericidal and antiviral activities. Complexes of partially unfolded α-LA with oleic acid are cytotoxic to various tumor and bacterial cells. α-LA in the cytotoxic complexes plays a role of a delivery carrier of cytotoxic fatty acid molecules into tumor and bacterial cells across the cell membrane. Perhaps in the future the complexes of α-LA with oleic acid will be used for development of new anti-cancer drugs.
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Wodas L, Mackowski M, Borowska A, Puppel K, Kuczynska B, Cieslak J. Genes encoding equine β-lactoglobulin (LGB1 and LGB2): Polymorphism, expression, and impact on milk composition. PLoS One 2020; 15:e0232066. [PMID: 32320437 PMCID: PMC7176115 DOI: 10.1371/journal.pone.0232066] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 04/06/2020] [Indexed: 11/21/2022] Open
Abstract
β-lactoglobulin is one of the most abundant milk whey proteins in many mammal species, including the domestic horse. The aim of this study was to screen for polymorphism in the equine LGB1 and LGB2 gene sequences (all exons, introns, and 5’-flanking region) and to assess potential relationship of particular genotypes with gene expression levels (measured in milk somatic cells) and milk composition traits (protein, fat, lactose, and total β-lactoglobulin content). Direct DNA sequencing analysis was performed for twelve horse breeds: Polish Primitive Horse (PPH), Polish Coldblood Horse (PCH), Polish Warmblood Horse (PWH), Silesian, Hucul, Fjording, Haflinger, Shetland Pony, Welsh Pony, Arabian, Thoroughbred, and Percheron—and revealed the presence of 83 polymorphic sites (47 and 36 for LGB1 and LGB2 genes, respectively), including eight that were previously unknown. Association analysis of the selected polymorphisms, gene expression, and milk composition traits (conducted for the PPH, PCH, and PWH breeds) showed several statistically significant relationships; for example, the two linked LGB1 SNPs (rs1143515669 and rs1144647991) were associated with total milk protein content (p < 0.01). Our study also confirmed that horse breed had significant impact on both gene transcript levels (p < 0.01) and on milk LGB content (p < 0.05), whereas an influence of lactation period was seen only for gene relative mRNA abundances (p < 0.01).
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Affiliation(s)
- Lukasz Wodas
- Department of Horse Breeding, Poznan University of Life Sciences, Poznan, Poland
| | - Mariusz Mackowski
- Department of Horse Breeding, Poznan University of Life Sciences, Poznan, Poland
- Horse Genetic Markers Laboratory, Poznan University of Life Sciences, Poznan, Poland
| | - Alicja Borowska
- Department of Horse Breeding, Poznan University of Life Sciences, Poznan, Poland
| | - Kamila Puppel
- Cattle Breeding Division, Department of Animal Science, Warsaw University of Life Sciences, Warsaw, Poland
| | - Beata Kuczynska
- Cattle Breeding Division, Department of Animal Science, Warsaw University of Life Sciences, Warsaw, Poland
| | - Jakub Cieslak
- Department of Horse Breeding, Poznan University of Life Sciences, Poznan, Poland
- * E-mail:
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Allele and Genotype Frequencies of the Κappa-Casein (CSN3) Locus in Macedonian Holstein-Friesian Cattle. MACEDONIAN VETERINARY REVIEW 2020. [DOI: 10.2478/macvetrev-2020-0013] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Abstract
The bovine kappa-casein (κ-CN) is a phospho-protein with 169 amino acids encoded by the CSN3 gene. The two most common gene variants in the HF breed are CSN3*A and CSN3*B while CSN3*E has been found with lower frequency. The aim of this study was to optimize a laboratory method for genotyping of these three alleles as well as to determine their genotype and allele frequencies in the HF cattle population in the Republic of North Macedonia. Genomic DNA was extracted from full blood from 250 cows. The target DNA sequence was amplified with newly designed pair of primers and the products were subjected to enzymatic restriction with HindIII and HaeIII endonucleases. Genotype determination was achieved in all animals. The primers successfully amplified a fragment of 458 bp and the digestion of this fragment with both endonucleases enabled differentiation of five different genotypes with the following observed frequencies: AA (0.39), AB (0.29), BB (0.16), AE (0.10), and BE (0.06). The estimated allele frequencies were: CSN3*A (0.584), CSN3*B (0.336) and CSN3*E (0.08). The observed genotype frequencies differed significantly (P<0.01) from those that would be expected under HW equilibrium, while the fixation index (F=0.17) indicated moderate heterozygosity deficiency. Nevertheless, the CSN3*B allele was present with relatively high frequency which should be used to positively select for its carriers, since increasing its frequency could help to improve the rheological properties of the milk intended for cheese production.
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Summer A, Di Frangia F, Ajmone Marsan P, De Noni I, Malacarne M. Occurrence, biological properties and potential effects on human health of β-casomorphin 7: Current knowledge and concerns. Crit Rev Food Sci Nutr 2020; 60:3705-3723. [PMID: 32033519 DOI: 10.1080/10408398.2019.1707157] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The genetic variant A1 of bovine β-casein (β-Cn) presents a His residue at a position 67 of the mature protein. This feature makes the Ile66-His67 bond more vulnerable to enzymatic cleavage, determining the release of the peptide β-Cn f(60-66), named β-casomorphin 7 (BCM7). BCM7 is an opioid-agonist for μ receptors, and it has been hypothesized to be involved in the development of different non-transmissible diseases in humans. In the last decade, studies have provided additional results on the potential health impact of β-Cn A1 and BCM7. These studies, here reviewed, highlighted a relation between the consumption of β-Cn A1 (and its derivative BCM7) and the increase of inflammatory response as well as discomfort at the gastrointestinal level. Conversely, the role of BCM7 and the effects of ingestion of β-Cn A1 on the onset or worsening of other non-transmissible diseases as caused or favored by still need proof of evidence. Overall, the reviewed literature demonstrates that the "β-Cn A1/BCM7 issue" remains an intriguing but not exhaustively explained topic in human nutrition. On this basis, policies in favor of breeding for β-Cn variants not releasing BCM7 and consumption of "A1-like" milk appear not yet sound for a healthier and safer nutrition.
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Affiliation(s)
- Andrea Summer
- Department of Veterinary Sciences, Università di Parma, Parma, Italy
| | | | - Paolo Ajmone Marsan
- Department of Animal Science, Food and Nutrition (DIANA) and Nutrigenomics and Proteomics Research Center (PRONUTRIGEN), Università Cattolica del Sacro Cuore, Piacenza, Italy
| | - Ivano De Noni
- Department of Food, Environmental and Nutritional Sciences (DeFENS), Università degli Studi di Milano, Milan, Italy
| | - Massimo Malacarne
- Department of Veterinary Sciences, Università di Parma, Parma, Italy
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Meier S, Korkuć P, Arends D, Brockmann GA. DNA Sequence Variants and Protein Haplotypes of Casein Genes in German Black Pied Cattle (DSN). Front Genet 2019; 10:1129. [PMID: 31781175 PMCID: PMC6857469 DOI: 10.3389/fgene.2019.01129] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Accepted: 10/17/2019] [Indexed: 11/13/2022] Open
Abstract
Casein proteins were repeatedly examined for protein polymorphisms and frequencies in diverse cattle breeds. The occurrence of casein variants in Holstein Friesian, the leading dairy breed worldwide, is well known. The frequencies of different casein variants in Holstein are likely affected by selection for high milk yield. Compared to Holstein, only little is known about casein variants and their frequencies in German Black Pied cattle (“Deutsches Schwarzbuntes Niederungsrind,” DSN). The DSN population was a main genetic contributor to the current high-yielding Holstein population. The goal of this study was to investigate casein (protein) variants and casein haplotypes in DSN based on the DNA sequence level and to compare these with data from Holstein and other breeds. In the investigated DSN population, we found no variation in the alpha-casein genes CSN1S1 and CSN1S2 and detected only the CSN1S1*B and CSN1S2*A protein variants. For CSN2 and CSN3 genes, non-synonymous single nucleotide polymorphisms leading to three different β and κ protein variants were found, respectively. For β-casein protein variants A1, A2, and I were detected, with CSN2*A1 (82.7%) showing the highest frequency. For κ-casein protein variants A, B, and E were detected in DSN, with the highest frequency of CSN3*A (83.3%). Accordingly, the casein protein haplotype CSN1S1*B-CSN2*A1-CSN1S2*A-CSN3*A (order of genes on BTA6) is the most frequent haplotype in DSN cattle.
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Affiliation(s)
- Saskia Meier
- Faculty of Life Sciences, Albrecht Daniel Thaer Institute for Agricultural and Horticultural Sciences, Animal Breeding Biology and Molecular Genetics, Humboldt University of Berlin, Berlin, Germany
| | - Paula Korkuć
- Faculty of Life Sciences, Albrecht Daniel Thaer Institute for Agricultural and Horticultural Sciences, Animal Breeding Biology and Molecular Genetics, Humboldt University of Berlin, Berlin, Germany
| | - Danny Arends
- Faculty of Life Sciences, Albrecht Daniel Thaer Institute for Agricultural and Horticultural Sciences, Animal Breeding Biology and Molecular Genetics, Humboldt University of Berlin, Berlin, Germany
| | - Gudrun A Brockmann
- Faculty of Life Sciences, Albrecht Daniel Thaer Institute for Agricultural and Horticultural Sciences, Animal Breeding Biology and Molecular Genetics, Humboldt University of Berlin, Berlin, Germany
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Lu H, Bovenhuis H. Genome-wide association studies for genetic effects that change during lactation in dairy cattle. J Dairy Sci 2019; 102:7263-7276. [PMID: 31155265 DOI: 10.3168/jds.2018-15994] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Accepted: 04/04/2019] [Indexed: 11/19/2022]
Abstract
Genetic effects on milk production traits in dairy cattle might change during lactation. However, most genome-wide association studies (GWAS) for milk production traits assume that genetic effects are constant during lactation. This assumption might lead to missing these quantitative trait loci (QTL) whose effects change during lactation. This study aimed to screen the whole genome specifically for QTL whose effects change during lactation. For this purpose, 4 different GWAS approaches were performed using test-day milk protein content records: (1) separate GWAS for specific lactation stages, (2) GWAS for estimated Wilmink lactation curve parameters, (3) a GWAS using a repeatability model where SNP effects are assumed constant during lactation, and (4) a GWAS for genotype by lactation stage interaction using a repeatability model and accounting for changing genetic effects during lactation. Separate GWAS for specific lactation stages suggested that the detection power greatly differs between lactation stages and that genetic effects of some QTL change during lactation. The GWAS for estimated Wilmink lactation curve parameters detected many chromosomal regions for Wilmink parameter a (protein content level), whereas 2 regions for Wilmink parameter b (decrease in protein content toward nadir) and no regions for Wilmink parameter c (increase in protein content after nadir) were detected. Twenty chromosomal regions were detected with effects on milk protein content; however, there was no evidence that their effects changed during lactation. For 5 chromosomal regions located on chromosomes 3, 9, 10, 14, and 27, significant evidence was observed for a genotype by lactation stage interaction and thus their effects on milk protein content changed during lactation. Three of these 5 regions were only identified using a GWAS for genotype by lactation stage interaction. Our study demonstrated that GWAS for genotype by lactation stage interaction offers new possibilities to identify QTL involved in milk protein content. The performed approaches can be applied to other milk production traits. Identification of QTL whose genetic effects change during lactation will help elucidate the genetic and biological background of milk production.
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Affiliation(s)
- Haibo Lu
- Animal Breeding and Genomics, Wageningen University and Research, PO Box 338, 6700 AH, Wageningen, the Netherlands
| | - Henk Bovenhuis
- Animal Breeding and Genomics, Wageningen University and Research, PO Box 338, 6700 AH, Wageningen, the Netherlands.
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Ryskaliyeva A, Henry C, Miranda G, Faye B, Konuspayeva G, Martin P. Alternative splicing events expand molecular diversity of camel CSN1S2 increasing its ability to generate potentially bioactive peptides. Sci Rep 2019; 9:5243. [PMID: 30918277 PMCID: PMC6437144 DOI: 10.1038/s41598-019-41649-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Accepted: 03/14/2019] [Indexed: 02/08/2023] Open
Abstract
In a previous study on camel milk from Kazakhstan, we reported the occurrence of two unknown proteins (UP1 and UP2) with different levels of phosphorylation. Here we show that UP1 and UP2 are isoforms of camel αs2-CN (αs2-CNsv1 and αs2-CNsv2, respectively) arising from alternative splicing events. First described as a 178 amino-acids long protein carrying eight phosphate groups, the major camel αs2-CN isoform (called here αs2-CN) has a molecular mass of 21,906 Da. αs2-CNsv1, a rather frequent (35%) isoform displaying a higher molecular mass (+1,033 Da), is present at four phosphorylation levels (8P to 11P). Using cDNA-sequencing, αs2-CNsv1 was shown to be a variant arising from the splicing-in of an in-frame 27-nucleotide sequence encoding the nonapeptide ENSKKTVDM, for which the presence at the genome level was confirmed. αs2-CNsv2, which appeared to be present at 8P to 12P, was shown to include an additional decapeptide (VKAYQIIPNL) revealed by LC-MS/MS, encoded by a 3'-extension of exon 16. Since milk proteins represent a reservoir of biologically active peptides, the molecular diversity generated by differential splicing might increase its content. To evaluate this possibility, we searched for bioactive peptides encrypted in the different camel αs2-CN isoforms, using an in silico approach. Several peptides, putatively released from the C-terminal part of camel αs2-CN isoforms after in silico digestion by proteases from the digestive tract, were predicted to display anti-bacterial and antihypertensive activities.
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Affiliation(s)
- Alma Ryskaliyeva
- INRA, UMR GABI, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - Céline Henry
- INRA, MICALIS Institute, Plateforme d'Analyse Protéomique Paris Sud-Ouest (PAPPSO), Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - Guy Miranda
- INRA, UMR GABI, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - Bernard Faye
- CIRAD, UMR SELMET, 34398, Montpellier Cedex 5, France
| | - Gaukhar Konuspayeva
- Al-Farabi Kazakh National University, Biotechnology department, 050040, Almaty, Kazakhstan
| | - Patrice Martin
- INRA, UMR GABI, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France.
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17
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Ryskaliyeva A, Henry C, Miranda G, Faye B, Konuspayeva G, Martin P. The main WAP isoform usually found in camel milk arises from the usage of an improbable intron cryptic splice site in the precursor to mRNA in which a GC-AG intron occurs. BMC Genet 2019; 20:14. [PMID: 30696406 PMCID: PMC6350295 DOI: 10.1186/s12863-018-0704-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Accepted: 11/30/2018] [Indexed: 01/10/2023] Open
Abstract
Background Whey acidic protein (WAP) is a major protein identified in the milk of several mammalian species with cysteine-rich domains known as four-disulfide cores (4-DSC). The organization of the eutherian WAP genes is highly conserved through evolution. It has been proposed that WAP could play an important role in regulating the proliferation of mammary epithelial cells. A bacteriostatic activity was also reported. Conversely to the other mammalian species expressing WAP in their milk, camel WAP contains 4 additional amino acid residues at the beginning of the second 4-DSC domain, introducing a phosphorylation site. The aim of this study was to elucidate the origin of this specificity, which possibly impacts its physiological functions. Results Using LC-ESI-MS, we identified in Camelus bactrianus from Kazakhstan a phosphorylated whey protein, exhibiting a molecular mass (12,596 Da), 32 Da higher than the original WAP (12,564 Da) and co-eluting with WAP. cDNA sequencing revealed a transition G/A, which modifies an amino acid residue of the mature protein (V12 M), accounting for the mass difference observed between WAP genetic variants. We also report the existence of two splicing variants of camel WAP precursors to mRNA, arising from an alternative usage of the canonical splice site recognized as such in the other mammalian species. However, the major camel WAP isoform results from the usage of an unlikely intron cryptic splice site, extending camel exon 3 upstream by 12-nucleotides encoding the 4 additional amino acid residues (VSSP) in which a potentially phosphorylable Serine residue occurs. Combining protein and cDNA sequences with genome data available (NCBI database), we report another feature of the camel WAP gene which displays a very rare GC-AG type intron. This result was confirmed by sequencing a genomic DNA fragment encompassing exon 3 to exon 4, suggesting for the GC donor site a compensatory effect in terms of consensus at the acceptor exon position. Conclusions Combining proteomic and molecular biology approaches we report: the characterization of a new genetic variant of camel WAP, the usage of an unlikely intron cryptic splice site, and the occurrence of an extremely rare GC-AG type of intron.
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Affiliation(s)
- Alma Ryskaliyeva
- INRA, UMR GABI, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - Céline Henry
- Plateforme d'Analyse Protéomique Paris Sud-Ouest (PAPPSO), INRA, MICALIS Institute, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - Guy Miranda
- INRA, UMR GABI, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - Bernard Faye
- CIRAD, UMR SELMET, 34398, Montpellier Cedex 5, France
| | - Gaukhar Konuspayeva
- Biological Technology Department, Al-Farabi Kazakh National University, Almaty, Kazakhstan
| | - Patrice Martin
- INRA, UMR GABI, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France.
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18
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Abstract
Genetic improvement is constrained by the long-term and cumulate nature of genetic improvement, by the economic rewards for making genetic change and by the variances and covariances among traits of interest. Genetic change is cumulate, so that small annual changes make substantial differences over time. This cumulate nature of genetic improvement dictates the importance of identifying long-term goals driven by robust economic signals and then adhering to them. The economic rewards for genetic improvement will ultimately determine the uptake and therefore the success of any breeding program. In developed countries the value of milk can be divided between the weight of water, fat and protein produced. Water generally has a negative value due the cost of handling, removal and disposal. Fat and protein have varying values depending on the market, but both will always have underlying positive values. Genetic variances and covariances among the aggregate composition traits, water, fat and protein, are such that simultaneous increase in the yield of all three is considerably easier than improvement of just one, or improvement of one while decreasing others. Selection for simultaneous increase of fat and protein percentage will also be successful, but at the price of not increasing fat and protein yield nearly as rapidly as when selecting directly on yield traits. In virtually all developed countries, the optimum selection goal will be for some combination of increased fat and protein yield that may lead to a gradual increase in the protein to fat ratio. Genetic polymorphisms in several protein genes have been associated with yield and with milk processing properties, but are unlikely to play more than a minor role in overall selection. There is some evidence of genetic variation in milk fat composition, but the level of variation and economic incentives for change mean that selection for milk fat composition is not worthwhile. Thus, with the exception of very slow changes in the water to fat to protein yield ratio, genetic improvement does not seem a particularly suitable route for altering milk composition.
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19
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Patel JB, Chauhan JB. Computational analysis of non-synonymous single nucleotide polymorphism in the bovine cattle kappa-casein (CSN3) gene. Meta Gene 2018. [DOI: 10.1016/j.mgene.2017.10.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
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20
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Effects of different genotypes at the CSN3 and LGB loci on milk and cheese-making characteristics of the bovine Cinisara breed. Int Dairy J 2017. [DOI: 10.1016/j.idairyj.2016.11.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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21
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Trujillo A, Jordana J, Guamis B, Serradilla J, Amills M. Revisión: E1 polimorfismo del gen de la caseina αs1 caprina y su efecto sobre la producción, la composición y las propiedades tecnológicas de la leche y sobre la fabricación y la maduración del queso. FOOD SCI TECHNOL INT 2016. [DOI: 10.1177/108201329800400401] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
The caprine α s1-casein gene displays a high degree of polymorphism, with eight different protein variants described up to date. The rate of synthesis of the mature protein is closely linked to the caprine αs1-casein genotype. There are three variants which are associated to high αs1-casein content in milk (A, B, and C), one to an intermediate content (E), three to a low content (D, F, and G) and one to a null content (O). During the last few years studies of goat milk protein polymorphism have gained renewed interest, as the ocurrence of certain milk protein genetic variants is correlated with the composititon of milk and also with some milk processing parameters. For instance, analyses of the physicochemical properties of milk from goats homozy gous for the three main α s1-casein alleles (A, E, F) confirm the effects of the genotypes on the percentage of casein and fat, and shows significant effects on the diameter of the micelles and their calcium content. These characteristics seem to be associated with enhanced clotting of goat milk, cheese curd firmness, curd syneresis and overall cheese yield. The caprine αs1-casein gene constitutes a very attractive model for studying the regulation of the expression of the corresponding protein, and might also become a very powerful tool in improving the technolog ical properties of goat milk.
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Affiliation(s)
- A.J. Trujillo
- Unitat de Tecnologia dels Aliments. Centre Especial de Referència en Làctis. Facultat de Veterinària, Universitat Autònoma de Barcelona. Bellaterra 08193. Spain
| | - J. Jordana
- Unitat de Genètica i Millora. Facultat de Veterinària. Universitat Autònoma de Barcelona. Bellaterra 08193. Spain
| | - B. Guamis
- Unitat de Tecnologia dels Aliments. Centre Especial de Referència en Làctis. Facultat de Veterinària, Universitat Autònoma de Barcelona. Bellaterra 08193. Spain
| | - J.M. Serradilla
- Departamento de Producción Animal. Escuela Técnica Superior de Ingenieros Agrónomos y de Montes., Universidad de Córdoba. Córdoba 14080. Spain
| | - M. Amills
- Unitat de Genètica i Millora. Facultat de Veterinària. Universitat Autònoma de Barcelona. Bellaterra 08193. Spain
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22
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Calus MPL, Bouwman AC, Schrooten C, Veerkamp RF. Efficient genomic prediction based on whole-genome sequence data using split-and-merge Bayesian variable selection. Genet Sel Evol 2016; 48:49. [PMID: 27357580 PMCID: PMC4926307 DOI: 10.1186/s12711-016-0225-x] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2016] [Accepted: 06/16/2016] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Use of whole-genome sequence data is expected to increase persistency of genomic prediction across generations and breeds but affects model performance and requires increased computing time. In this study, we investigated whether the split-and-merge Bayesian stochastic search variable selection (BSSVS) model could overcome these issues. BSSVS is performed first on subsets of sequence-based variants and then on a merged dataset containing variants selected in the first step. RESULTS We used a dataset that included 4,154,064 variants after editing and de-regressed proofs for 3415 reference and 2138 validation bulls for somatic cell score, protein yield and interval first to last insemination. In the first step, BSSVS was performed on 106 subsets each containing ~39,189 variants. In the second step, 1060 up to 472,492 variants, selected from the first step, were included to estimate the accuracy of genomic prediction. Accuracies were at best equal to those achieved with the commonly used Bovine 50k-SNP chip, although the number of variants within a few well-known quantitative trait loci regions was considerably enriched. When variant selection and the final genomic prediction were performed on the same data, predictions were biased. Predictions computed as the average of the predictions computed for each subset achieved the highest accuracies, i.e. 0.5 to 1.1 % higher than the accuracies obtained with the 50k-SNP chip, and yielded the least biased predictions. Finally, the accuracy of genomic predictions obtained when all sequence-based variants were included was similar or up to 1.4 % lower compared to that based on the average predictions across the subsets. By applying parallelization, the split-and-merge procedure was completed in 5 days, while the standard analysis including all sequence-based variants took more than three months. CONCLUSIONS The split-and-merge approach splits one large computational task into many much smaller ones, which allows the use of parallel processing and thus efficient genomic prediction based on whole-genome sequence data. The split-and-merge approach did not improve prediction accuracy, probably because we used data on a single breed for which relationships between individuals were high. Nevertheless, the split-and-merge approach may have potential for applications on data from multiple breeds.
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Affiliation(s)
- Mario P L Calus
- Animal Breeding and Genomics Centre, Wageningen UR Livestock Research, PO Box 338, 6700 AH, Wageningen, The Netherlands.
| | - Aniek C Bouwman
- Animal Breeding and Genomics Centre, Wageningen UR Livestock Research, PO Box 338, 6700 AH, Wageningen, The Netherlands
| | | | - Roel F Veerkamp
- Animal Breeding and Genomics Centre, Wageningen UR Livestock Research, PO Box 338, 6700 AH, Wageningen, The Netherlands
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Singh LV, Jayakumar S, Sharma A, Gupta SK, Dixit SP, Gupta N, Gupta SC. Comparative screening of single nucleotide polymorphisms in β-casein and κ-casein gene in different livestock breeds of India. Meta Gene 2015; 4:85-91. [PMID: 25905036 PMCID: PMC4401812 DOI: 10.1016/j.mgene.2015.03.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2015] [Revised: 03/17/2015] [Accepted: 03/18/2015] [Indexed: 11/28/2022] Open
Abstract
The most polymorphic milk protein gene is β-casein; 13 protein variants are known in cattle. Milk protein genetic polymorphism has received considerable research interest in recent years because of possible associations between milk protein and economically important traits in livestock. The present study was undertaken to explore the genetic polymorphisms in exon 7 of β-casein and exon 4 of κ-casein genes in Arunachali yaks (Bos grunniens), Sahiwal (Bos indicus) cattle, malpura sheep (Ovis aries) and Gaddi goat (Capra hircus). Results of the study revealed presence of 11 SNP variants in all livestock species. Four SNPs were observed in Bos indicus; two SNPs in Bos grunniens; three SNPs in Ovis aries and three SNPs in Capra hircus. These variations are found to be synonymous in nature as these variations do not result in their corresponding amino acids. A total of five polymorphic sites have been described at the κ-casein (CSN3) locus in the Indian domestic Gaddi goat (Capra hircus) when compared with exotic goat (X60763) while sequence analysis of κ-casein gene in sheep showed three novel nucleotide changes in malpura sheep when compared with the exotic sheep (AY237637). These results highlight the importance of taking into consideration the CSN3 SNPs when performing selection for milk composition in dairy livestock breeds. This is first comparative sequence analysis of Beta casein and kappa casein genes in different livestock breeds of India. Total 11 SNPs variants were found in all livestock species studied, namely, Bos indicus, Bos grunniens, Ovis aries and Capra hircus. Four SNPs were observed in Bos indicus; two SNPs in Bos grunniens; three SNPs in Ovis aries and three SNPs in Capra hircus. Homology of 99% with Bos taurus and Bos indicus, 97% with Bubalus bubaline, 99% with Bos grunniens, 95% with Ovis aries, 95% with Capra hircus. Sequence analysis of κ-casein gene in sheep showed three novel nucleotide changes in malpura sheep when compared with the exotic sheep (AY237637).
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Affiliation(s)
- Lakshya Veer Singh
- DNA Fingerprinting Unit, National Bureau of Animal Genetic Resources, Karnal 132001, India ; Division of Veterinary Biotechnology, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, India
| | - S Jayakumar
- DNA Fingerprinting Unit, National Bureau of Animal Genetic Resources, Karnal 132001, India
| | - Anurodh Sharma
- DNA Fingerprinting Unit, National Bureau of Animal Genetic Resources, Karnal 132001, India
| | - Shishir Kumar Gupta
- Division of Veterinary Biotechnology, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, India
| | - S P Dixit
- DNA Fingerprinting Unit, National Bureau of Animal Genetic Resources, Karnal 132001, India
| | | | - S C Gupta
- Krishi Bhawan, ICAR, New Delhi, India
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Kishore A, Mukesh M, Sobti RC, Kataria RS, Mishra BP, Sodhi M. Analysis of genetic variations across regulatory and coding regions of kappa-casein gene of Indian native cattle (Bos indicus) and buffalo (Bubalus bubalis). Meta Gene 2014; 2:769-81. [PMID: 25606460 PMCID: PMC4287854 DOI: 10.1016/j.mgene.2014.10.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2014] [Revised: 09/20/2014] [Accepted: 10/04/2014] [Indexed: 12/04/2022] Open
Abstract
The promoter region of kappa-casein (κ-CN) gene in Indian native cattle and buffalo breeds was sequenced and analyzed for nucleotide variations. Sequence comparison across breeds of Indian cattle revealed a total of 7 variations in the promoter region, of which − 515 G/T, − 427 C/T, − 385 C/T, − 283 A/G and − 251 C/T were located within consensus binding sites for octamer-binding protein (OCT1)/pregnancy specific mammary nuclear factor (PMF), activator protein-2 (AP2), hepatocyte nuclear factor (HNF-1) and GAL4 transcription factors (TFs), respectively. These variations might be involved in gain or loss of potential transcription factor binding sites (TFBSs). Unlike the other 4 variants, the − 283 (A/G) variant located within HNF-1 TFBS was specific to Indian cattle as this change has not been observed in the Bos taurus sequence. Other TFBSs viz., MGF, TBP, NF-1, milk box and C/EBP were conserved across species. For the Indian native buffalo breeds, only 3 changes were identified in the promoter region; − 305 (A/C), − 160 (T/C) and − 141 (A/G) and most of the TFBSs were found to be conserved. However, deletion of two adjacent nucleotides located in and around binding site for C/EBP TF was identified in buffalo when compared with promoter sequence of bovine κ-CN. For κ-CN of Indian native cattle, a strong linkage disequilibrium (LD) was observed for variations 515 G/T, − 427 C/T and − 385 C/T in the promoter region; and for variations at codons 136 and 148 of exon-IV. Further, among intragenic haplotypes, variation − 427 C/T was found to be in LD with variations at codons 136 and 148. The information generated in the present work provides comprehensive characterization of κ-CN gene promoter and coding regions in Indian cattle and buffaloes and reported variations could become important candidates for carrying out further research in dairy traits. The κ-casein gene (κ-CN) and its promoter region was sequence characterized in 15 Indian native cattle and 8 buffalo breeds. Among the identified variations, four were located within TFBSs in Indian cattle, while all TFBSs were conserved in buffaloes. The κ-CN CDS was highly conserved with only 3 and 2 non-synonymous changes for Indian cattle and buffaloes, respectively. Across promoter and CDS, − 427 C/T was found to be in LD with variation at codons 136 and 148.
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Affiliation(s)
- Amit Kishore
- National Bureau of Animal Genetics Resources, PO Box-129, Karnal 132 001, Haryana, India ; Department of Biotechnology, Panjab University, Chandigarh 160 014, India
| | - M Mukesh
- National Bureau of Animal Genetics Resources, PO Box-129, Karnal 132 001, Haryana, India
| | - R C Sobti
- Department of Biotechnology, Panjab University, Chandigarh 160 014, India
| | - R S Kataria
- National Bureau of Animal Genetics Resources, PO Box-129, Karnal 132 001, Haryana, India
| | - B P Mishra
- National Bureau of Animal Genetics Resources, PO Box-129, Karnal 132 001, Haryana, India
| | - Monika Sodhi
- National Bureau of Animal Genetics Resources, PO Box-129, Karnal 132 001, Haryana, India
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25
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Milk protein variants are highly associated with milk performance traits in East Friesian Dairy and Lacaune sheep. Small Rumin Res 2014. [DOI: 10.1016/j.smallrumres.2014.09.001] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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26
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Bijl E, van Valenberg HJF, Huppertz T, van Hooijdonk ACM, Bovenhuis H. Phosphorylation of αS1-casein is regulated by different genes. J Dairy Sci 2014; 97:7240-6. [PMID: 25200775 DOI: 10.3168/jds.2014-8061] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2014] [Accepted: 07/10/2014] [Indexed: 11/19/2022]
Abstract
Casein phosphorylation is a posttranslational modification catalyzed by kinase enzymes that attach phosphate groups to specific AA in the protein sequence. This modification is one of the key factors responsible for the stabilization of calcium phosphate nanoclusters in casein micelles and for the internal structure of the casein micelles. α(S1)-Casein (α(s1)-CN) is of special interest because it constitutes up to 40% of the total casein fraction in milk, and it has 2 common phosphorylation states, with 8 (α(S1)-CN-8P) and 9 (α(S1)-CN-9P) phosphorylated serine residues. Factors affecting this variation in the degree of phosphorylation are not currently known. The objective of this research was to determine the genetic background of α(S1)-CN-8P and α(S1)-CN-9P. The genetic and phenotypic correlation between α(S1)-CN-8P and α(S1)-CN-9P was low (0.18 and 0.19, respectively). This low genetic correlation suggests a different genetic background. These differences were further investigated by means of a genome-wide association study, which showed that both α(S1)-CN-8P and α(S1)-CN-9P were affected by a region on Bos taurus autosome (BTA) 6, but only α(S1)-CN-8P was affected by a region on BTA11 that contains the gene that encodes for β-lactoglobulin (β-LG), and only α(S1)-CN-9P was affected by a region on BTA14 that contains the diacylglycerol acyltransferase 1 (DGAT1) gene. Estimated effects of β-LG protein genotypes showed that only α(S1)-CN-8P was associated with the β-LG A/B polymorphism (g.1772G>A and g.3054C>T); the AA genotype of β-LG was associated with a lower concentration of α(S1)-CN-8P (-0.32% wt/wt) than the BB genotype (+0.41% wt/wt). Estimated effects of DGAT1 K232A genotypes showed that only α(S1)-CN-9P was associated with the DGAT1 gene polymorphism; DGAT1 AA genotype was associated with a higher α(S1)-CN-9P concentration (+0.53% wt/wt) than the DGAT1 KK genotype (-0.44% wt/wt). The results give insight in phosphorylation of α(S1)-CN-8P and α(S1)-CN-9P, which seem to be regulated by a different set of genes.
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Affiliation(s)
- E Bijl
- Dairy Science and Technology Group, Wageningen University, PO Box 17, 6700 AA, Wageningen, the Netherlands
| | - H J F van Valenberg
- Dairy Science and Technology Group, Wageningen University, PO Box 17, 6700 AA, Wageningen, the Netherlands
| | - T Huppertz
- NIZO Food Research, PO Box 20, 6710 BA, Ede, the Netherlands
| | - A C M van Hooijdonk
- Dairy Science and Technology Group, Wageningen University, PO Box 17, 6700 AA, Wageningen, the Netherlands
| | - H Bovenhuis
- Animal Breeding and Genomics Centre, Wageningen University, PO Box 338, 6700 AH, Wageningen, the Netherlands.
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27
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Effect of polymorphisms in the CSN3 (κ-casein) gene on milk production traits in Chinese Holstein Cattle. Mol Biol Rep 2014; 41:7585-93. [DOI: 10.1007/s11033-014-3648-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2013] [Accepted: 07/27/2014] [Indexed: 02/07/2023]
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Yue XP, Fang Q, Zhang X, Mao CC, Lan XY, Chen H, Lei CZ. Effects of CSN1S2 Genotypes on Economic Traits in Chinese Dairy Goats. ASIAN-AUSTRALASIAN JOURNAL OF ANIMAL SCIENCES 2014; 26:911-5. [PMID: 25049867 PMCID: PMC4093498 DOI: 10.5713/ajas.2013.13018] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/06/2013] [Revised: 03/21/2013] [Accepted: 03/12/2013] [Indexed: 11/27/2022]
Abstract
The aim of this study was to investigate allele frequencies at the CSN1S2 locus in two Chinese dairy goat breeds and the effects of its variation on dairy goat economic traits. Seven hundred and eight goats from Xinong Saanen (XS, n = 268) and Guanzhong (GZ, N = 440) breeds were selected. The milk samples of 268 XS goats were collected during the middle of lactation, body size parameters (708 goats) and daily milk yield (202 goats) were registered. The RFLP (restriction fragment length polymorphism) and SSCP (single strand conformation polymorphism) were used to detect the polymorphisms in CSN1S2. The Hardy-Weinberg (HW) equilibrium and the associations between body size, milk yield and composition and the genotypes were calculated. The results revealed that only A and F CSN1S2 alleles were found in the two Chinese dairy goat breeds. Allelic frequencies of A and F were 0.795, 0.205 and 0.739, 0.261 in Xinong Saanen and Guanzhong population respectively. Xinong Saanen breed was in Hardy-Weinberg equilibrium, while Guanzhong breed deviated from Hardy-Weinberg equilibrium (p<0.05). The association of polymorphism with economic traits indicated that the goats with FF genotype have higher milk fat and total solid concentration than those with AA and AF genotypes (p<0.05).
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Affiliation(s)
- X P Yue
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Q Fang
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - X Zhang
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - C C Mao
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - X Y Lan
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - H Chen
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - C Z Lei
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
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Hristov P, Teofanova D, Mehandzhiyski I, Yoveva A, Radoslavov G. Genotyping of Endemic for Rhodopa Mountains Shorthorn Rhodopean Cow Breed. BIOTECHNOL BIOTEC EQ 2014. [DOI: 10.5504/50yrtimb.2011.0003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
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Major proteins in goat milk: an updated overview on genetic variability. Mol Biol Rep 2014; 41:1035-48. [DOI: 10.1007/s11033-013-2949-9] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2013] [Accepted: 12/20/2013] [Indexed: 11/25/2022]
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31
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Poulsen NA, Bertelsen HP, Jensen HB, Gustavsson F, Glantz M, Månsson HL, Andrén A, Paulsson M, Bendixen C, Buitenhuis AJ, Larsen LB. The occurrence of noncoagulating milk and the association of bovine milk coagulation properties with genetic variants of the caseins in 3 Scandinavian dairy breeds. J Dairy Sci 2013; 96:4830-42. [PMID: 23746587 DOI: 10.3168/jds.2012-6422] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2012] [Accepted: 04/22/2013] [Indexed: 11/19/2022]
Abstract
Substantial variation in milk coagulation properties has been observed among dairy cows. Consequently, raw milk from individual cows and breeds exhibits distinct coagulation capacities that potentially affect the technological properties and milk processing into cheese. This variation is largely influenced by protein composition, which is in turn affected by underlying genetic polymorphisms in the major milk proteins. In this study, we conducted a large screening on 3 major Scandinavian breeds to resolve the variation in milk coagulation traits and the frequency of milk with impaired coagulation properties (noncoagulation). In total, individual coagulation properties were measured on morning milk collected from 1,299 Danish Holstein (DH), Danish Jersey (DJ), and Swedish Red (SR) cows. The 3 breeds demonstrated notable interbreed differences in coagulation properties, with DJ cows exhibiting superior coagulation compared with the other 2 breeds. In addition, milk samples from 2% of DH and 16% of SR cows were classified as noncoagulating. Furthermore, the cows were genotyped for major genetic variants in the αS1- (CSN1S1), β- (CSN2), and κ-casein (CSN3) genes, revealing distinct differences in variant frequencies among breeds. Allele I of CSN2, which had not formerly been screened in such a high number of cows in these Scandinavian breeds, showed a frequency around 7% in DH and DJ, but was not detected in SR. Genetic polymorphisms were significantly associated with curd firming rate and rennet coagulation time. Thus, CSN1S1 C, CSN2 B, and CSN3 B positively affected milk coagulation, whereas CSN2 A(2), in particular, had a negative effect. In addition to the influence of individual casein genes, the effects of CSN1S1-CSN2-CSN3 composite genotypes were also examined, and revealed strong associations in all breeds, which more or less reflected the single gene results. Overall, milk coagulation is under the influence of additive genetic variation. Optimal milk for future cheese production can be ensured by monitoring the frequency of unfavorable variants and thus preventing an increase in the number of cows producing milk with impaired coagulation. Selective breeding for variants associated with superior milk coagulation can potentially increase raw milk quality and cheese yield in all 3 Scandinavian breeds.
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Affiliation(s)
- N A Poulsen
- Department of Food Science, Faculty of Science and Technology, Aarhus University, Tjele, Denmark.
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Identification of an intronic regulatory mutation at the buffalo αS1-casein gene that triggers the skipping of exon 6. Mol Biol Rep 2013; 40:4311-6. [PMID: 23640099 DOI: 10.1007/s11033-013-2518-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2012] [Accepted: 04/27/2013] [Indexed: 10/26/2022]
Abstract
The characterization of casein polymorphism is an essential step in order to understand the genetic basis of milk quality in dairy ruminants. In this work, we report the identification of a regulatory mutation at the buffalo αs1-casein (CSN1S1) gene that alters the normal processing of the primary transcript. Sequencing of CSN1S1 cDNA from individuals harbouring this new variant revealed that its most distinctive feature is the loss of exon 6 that encodes eight amino acids between positions 35-42 of mature protein. In an effort to map the causal mutation, we sequenced a genomic region spanning exons 5-7 of the buffalo CSN1S1 gene. This experiment allowed us to establish that exon 6-skipping is produced by a G to C substitution at the first position of intron 6 that inactivates the donor splice site. This mutation can be typed by PCR-RFLP by using either TaaI or Bpu10I diagnostic restriction enzymes, and it has a frequency of 0.18 in Romanian buffaloes. This exon skipping phenomenon is the first one described in buffalo CSN1S1 locus.
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Mastrangelo S, Sardina MT, Tolone M, Portolano B. Genetic polymorphism at the CSN1S1 gene in Girgentana dairy goat breed. ANIMAL PRODUCTION SCIENCE 2013. [DOI: 10.1071/an12242] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The aim of this work was to evaluate the variability of the αs1-casein locus in the endangered Girgentana dairy goat breed in order to define genetic improvement and a conservation program for this breed. The study was performed on 200 dairy goats by means of different PCR protocols. The most frequent alleles were A (0.590) and F (0.290) followed by B (0.065) and N (0.047). CSN1S1 E allele was identified with a very low frequency (0.008). The most common genotype was AF (0.365) followed by AA (0.340). The high frequency of the strong genotypes is associated with the production of milk with high fat and protein content and with optimal technological properties. In Girgentana goat breed, the CSN1S1 genotype information could be utilised in selection strategies for milk protein content and milk yield, in order to select genetic lines for the production of ‘drinking milk’ using weak and null genotypes, and for niche products using strong genotypes.
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Gallinat JL, Qanbari S, Drögemüller C, Pimentel ECG, Thaller G, Tetens J. DNA-based identification of novel bovine casein gene variants. J Dairy Sci 2012; 96:699-709. [PMID: 23102962 DOI: 10.3168/jds.2012-5908] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2012] [Accepted: 09/13/2012] [Indexed: 01/21/2023]
Abstract
In cattle, at least 39 variants of the 4 casein proteins (α(S1)-, β-, α(S2)- and κ-casein) have been described to date. Many of these variants are known to affect milk-production traits, cheese-processing properties, and the nutritive value of milk. They also provide valuable information for phylogenetic studies. So far, the majority of studies exploring the genetic variability of bovine caseins considered European taurine cattle breeds and were carried out at the protein level by electrophoretic techniques. This only allows the identification of variants that, due to amino acid exchanges, differ in their electric charge, molecular weight, or isoelectric point. In this study, the open reading frames of the casein genes CSN1S1, CSN2, CSN1S2, and CSN3 of 356 animals belonging to 14 taurine and 3 indicine cattle breeds were sequenced. With this approach, we identified 23 alleles, including 5 new DNA sequence variants, with a predicted effect on the protein sequence. The new variants were only found in indicine breeds and in one local Iranian breed, which has been phenotypically classified as a taurine breed. A multidimensional scaling approach based on available SNP chip data, however, revealed an admixture of taurine and indicine populations in this breed as well as in the local Iranian breed Golpayegani. Specific indicine casein alleles were also identified in a few European taurine breeds, indicating the introgression of indicine breeds into these populations. This study shows the existence of substantial undiscovered genetic variability of bovine casein loci, especially in indicine cattle breeds. The identification of new variants is a valuable tool for phylogenetic studies and investigations into the evolution of the milk protein genes.
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Affiliation(s)
- J L Gallinat
- Institute of Animal Breeding and Husbandry, Christian-Albrechts-University Kiel, D-24118 Kiel, Germany
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Abstract
The allelic distributions of the CSN1S1 (αs1-casein) in the Indian goats are quite different from European goat breeds. Majority of Indian goat breeds and non-descript goats carry A, B, E and F alleles at αs1-casein locus, as found by analysing both DNA and protein levels. However, A and B alleles, known to be associated with better casein yield, were observed in the highest proportion in all the Indian goat breeds. Gene frequency and breed heterozygosity were computed for the CSN1S1 gene. The gene frequency of allele A in Indian goats varies from 0.68 to 1.00 and allele B varies from 0.098 to 0.23. Allele F was observed in Beetal, Marwari, Chegu and non-descript goats of MP (Local MP) in less than 1% of population. The expected heterozygosity (He) varied from 0.141 to 0.506 over the population. The Beetal breed showed the highest gene diversity (0.506) followed by Jamunapari (0.395), Chegu (0.383) and Jakhrana (0.381) breeds. Therefore, the variability at CSN1S1 locus can be utilised for conservation as well as for genetic improvement of Indian goat breeds for increasing both the quality and quantity of milk production.
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Visker MHPW, Heck JML, van Valenberg HJF, van Arendonk JAM, Bovenhuis H. Short communication: A new bovine milk-protein variant: α-lactalbumin variant D. J Dairy Sci 2012; 95:2165-9. [PMID: 22459861 DOI: 10.3168/jds.2011-4794] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2011] [Accepted: 12/01/2011] [Indexed: 01/24/2023]
Abstract
Capillary zone electrophoresis of 1,948 Holstein-Friesian cows suggested the presence of an unknown protein variant of α-lactalbumin (α-LA) in the milk of 1 cow. Sequencing genomic DNA of this cow showed a polymorphism in the α-LA gene (LAA) that appears to be responsible for this protein variant. This single nucleotide polymorphism g.600G > T was located in exon 2 of LAA and causes the amino acid change 65Gln > His in the α-LA protein. This α-LA protein variant is a new protein variant and should be called α-LA protein variant D. This amino acid change is not expected to affect protein function. Genomic DNA of 156 bulls of various dairy cattle breeds was screened to examine the presence of the new α-LA protein variant D. Single nucleotide polymorphism g.600G > T, responsible for α-LA protein variant D, was not found in any of the 156 bulls. However, 10 other polymorphisms in the coding and promoter regions of LAA were detected that were used to construct haplotypes.
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Affiliation(s)
- M H P W Visker
- Animal Breeding and Genomics Centre, Wageningen University, PO Box 338, 6700 AH Wageningen, The Netherlands.
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Russell CD, Widdison S, Leigh JA, Coffey TJ. Identification of single nucleotide polymorphisms in the bovine Toll-like receptor 1 gene and association with health traits in cattle. Vet Res 2012; 43:17. [PMID: 22417166 PMCID: PMC3342155 DOI: 10.1186/1297-9716-43-17] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2011] [Accepted: 03/14/2012] [Indexed: 12/14/2022] Open
Abstract
Bovine mastitis remains the most common and costly disease of dairy cattle worldwide. A complementary control measure to herd hygiene and vaccine development would be to selectively breed cattle with greater resistance to mammary infection. Toll-like receptor 1 (TLR1) has an integral role for the initiation and regulation of the immune response to microbial pathogens, and has been linked to numerous inflammatory diseases. The objective of this study was to investigate whether single nucleotide polymorphisms (SNPs) within the bovine TLR1 gene (boTLR1) are associated with clinical mastitis (CM).Selected boTLR1 SNPs were analysed within a Holstein Friesian herd. Significant associations were found for the tagging SNP -79 T > G and the 3'UTR SNP +2463 C > T. We observed favourable linkage of reduced CM with increased milk fat and protein, indicating selection for these markers would not be detrimental to milk quality. Furthermore, we present evidence that some of these boTLR1 SNPs underpin functional variation in bovine TLR1. Animals with the GG genotype (from the tag SNP -79 T > G) had significantly lower boTLR1 expression in milk somatic cells when compared with TT or TG animals. In addition, stimulation of leucocytes from GG animals with the TLR1-ligand Pam3csk4 resulted in significantly lower levels of CXCL8 mRNA and protein.SNPs in boTLR1 were significantly associated with CM. In addition we have identified a bovine population with impaired boTLR1 expression and function. This may have additional implications for animal health and warrants further investigation to determine the suitability of identified SNPs as markers for disease susceptibility.
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Affiliation(s)
- Christopher D Russell
- Bovine Genomics Group, Institute for Animal Health, Compton, Berkshire, RG20 7NN, UK
- The School of Veterinary Medicine and Science, The University of Nottingham, Sutton Bonington Campus, Sutton Bonington, Leicestershire, LE12 5RD, UK
| | - Stephanie Widdison
- Bovine Genomics Group, Institute for Animal Health, Compton, Berkshire, RG20 7NN, UK
- The School of Veterinary Medicine and Science, The University of Nottingham, Sutton Bonington Campus, Sutton Bonington, Leicestershire, LE12 5RD, UK
| | - James A Leigh
- The School of Veterinary Medicine and Science, The University of Nottingham, Sutton Bonington Campus, Sutton Bonington, Leicestershire, LE12 5RD, UK
| | - Tracey J Coffey
- Bovine Genomics Group, Institute for Animal Health, Compton, Berkshire, RG20 7NN, UK
- The School of Veterinary Medicine and Science, The University of Nottingham, Sutton Bonington Campus, Sutton Bonington, Leicestershire, LE12 5RD, UK
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Frederiksen PD, Andersen KK, Hammershøj M, Poulsen HD, Sørensen J, Bakman M, Qvist KB, Larsen LB. Composition and effect of blending of noncoagulating, poorly coagulating, and well-coagulating bovine milk from individual Danish Holstein cows. J Dairy Sci 2012; 94:4787-99. [PMID: 21943730 DOI: 10.3168/jds.2011-4343] [Citation(s) in RCA: 92] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2011] [Accepted: 05/08/2011] [Indexed: 11/19/2022]
Abstract
The aim of the present investigation was to study the underlying causes of noncoagulating (NC) milk. Based on an initial screening in a herd of 53 Danish Holstein-Friesians, 20 individual Holstein-Friesian cows were selected for good and poor chymosin-induced coagulation properties; that is, the 10 cows producing milk with the poorest and best coagulating properties, respectively. These 20 selected cows were followed and resampled on several occasions to evaluate possible changes in coagulation properties. In the follow-up study, we found that among the 10 cows with the poorest coagulating properties, 4 cows consistently produced poorly coagulating (PC) or NC milk, corresponding to a frequency of 7%. Noncoagulating milk was defined as milk that failed to form a coagulum, defined as increase in the storage modulus (G') in oscillatory rheometry, within 45min after addition of chymosin. Poorly coagulating milk was characterized by forming a weak coagulum of low G'. Milk proteomic profiling and contents of different casein variants, ionic contents of Ca, P and Mg, κ-casein (CN) genotypes, casein micelle size, and coagulation properties of the 4 NC or PC samples were compared with milk samples of 4 cows producing milk with good coagulation properties. The studies included determination of production of caseinomacropeptide to ascertain whether noncoagulation could be ascribed to the first or second phase of chymosin-induced coagulation. Caseinomacropeptide was formed in all 8 milk samples after addition of chymosin, indicating that the first step (cleavage of κ-CN) was not the cause of inability to coagulate. Furthermore, the effect of mixing noncoagulating and well-coagulating milk was studied. By gradually blending NC with well-coagulating milk, the coagulation properties of the well-coagulating samples were compromised in a manner similar to titration. Milk samples from cows that consistently produced NC milk were further studied at the udder quarter level. The coagulation properties of the quarter milk samples were not significantly different from those of the composite milk sample, showing that poor coagulation traits and noncoagulation traits of the composite milk were not caused by the milk quality of a single quarter. The milk samples exhibiting PC or NC properties were all of the κ-CN variant AA genotype, and contained casein micelles with a larger mean diameter and a lower fraction of κ-CN relative to total CN than milk with good coagulation properties. Interestingly, the relative proportions of different phosphorylation forms of α-CN differed between well-coagulating milk and PC or NC milk samples. The PC and NC milk samples contained a lower proportion of the 2 less-phosphorylated variants of α-CN (α(S1)-CN-8P and α(S2)-CN-11P) compared with samples of milk that coagulated well.
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Affiliation(s)
- P D Frederiksen
- Department of Food Science, Faculty of Agricultural Sciences, Aarhus University, 8830 Tjele, Denmark
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Bonfatti V, Cecchinato A, Gallo L, Blasco A, Carnier P. Genetic analysis of detailed milk protein composition and coagulation properties in Simmental cattle. J Dairy Sci 2011; 94:5183-93. [DOI: 10.3168/jds.2011-4297] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2011] [Accepted: 06/23/2011] [Indexed: 11/19/2022]
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Abstract
ResumenEn el presente estudio se presentan los primeros resultados de la determinación de la estructura genética de tres poblaciones de ganado bovino autóctono cubano: Criollo de Cuba, Cebú Cubano y Siboney de Cuba, para los loci de seis proteínas lácteas (CASA1, CASAB, CASA2, CASK, LAA y LGB). Se analizaron un total de 150 individuos (50 por cada raza), mediante análisis de ADN por PCR-RFLP.Se calcularon las frecuencias alélicas para cadalocusasí como condiciones de equilibrio de Hardy-Weinberg. Fueron identificados los alelos CASA1Cy LAAAcomo evidencia de la presencia de genes deBos indicusen las tres poblaciones cubanas. Se comprobó la existencia de elevada variabilidad en cada población lo que constituye un elemento importante para trazar estrategias de mejoramiento y/o conservación genética.
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41
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Simianer H, Wild V. Effect and treatment of misclassified samples in linkage analysis*. J Anim Breed Genet 2011. [DOI: 10.1111/j.1439-0388.1995.tb00565.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Erhardt G, Juszczak J, Panicke L, Krick-Saleck H. Genetic polymorphism of milk proteins in Polish Red Cattle: a new genetic variant of β-lactoglobulin. J Anim Breed Genet 2011. [DOI: 10.1111/j.1439-0388.1998.tb00328.x] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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43
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Yue XP, Zhang XM, Wang W, Ma RN, Deng CJ, Lan XY, Chen H, Li F, Xu XR, Ma Y, Lei CZ. The CSN1S1 N and F alleles identified by PCR-SSCP and their associations with milk yield and composition in Chinese dairy goats. Mol Biol Rep 2010; 38:2821-5. [PMID: 21086177 DOI: 10.1007/s11033-010-0428-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2010] [Accepted: 11/08/2010] [Indexed: 11/25/2022]
Abstract
A method was depicted to identify null allele CSN1S1 N and low allele CSN1S1 F of the CSN1S1 gene of goat using PCR-SSCP (polymerase chain reaction-single strand conformation polymorphism). First, primer A was designed to amplify the exon 9 of CSN1S1 gene which produced three genotypes AA, AB, and BB. Among these three genotypes, only AA and AB individuals had a cytosine deletion at exon 9 after DNA sequencing, which cannot be used to identify the N and F alleles. Therefore, primer B was used to amplify intron 14 of CSN1S1 of described AA and AB individuals. Genotypes FF, FN and NN were detected within AA individuals and genotypes FO and NO were detected in the above AB individuals. The frequencies of F and N alleles in 708 samples from Xinong Saanen (XS) and Guanzhong (GZ) dairy goat breeds were 0.1139, 0.0927, and 0.2376, 0.1193, respectively. In 268 XS samples, the individuals with NN genotype contained a significant lower protein content than that of other genotypes (P<0.01). Individuals of FF genotype had significant higher milk yield than that of NO genotype in the first milk lactation of 202 XS individuals (P<0.05). Therefore, the variability at CSN1S1 locus contains enough genetic diversity to be potentially useful in improving the quality and production of milk in Chinese dairy goat breeds.
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Affiliation(s)
- X P Yue
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A & F University, No. 22 Xinong Road, Yangling, Shaanxi, 712100, People's Republic of China
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Bonfatti V, Di Martino G, Cecchinato A, Vicario D, Carnier P. Effects of β-κ-casein (CSN2-CSN3) haplotypes and β-lactoglobulin (BLG) genotypes on milk production traits and detailed protein composition of individual milk of Simmental cows. J Dairy Sci 2010; 93:3797-808. [DOI: 10.3168/jds.2009-2778] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2009] [Accepted: 04/08/2010] [Indexed: 11/19/2022]
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45
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Penasa M, Cassandro M, Pretto D, De Marchi M, Comin A, Chessa S, Dal Zotto R, Bittante G. Short communication: Influence of composite casein genotypes on additive genetic variation of milk production traits and coagulation properties in Holstein-Friesian cows. J Dairy Sci 2010; 93:3346-9. [DOI: 10.3168/jds.2010-3164] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2010] [Accepted: 03/29/2010] [Indexed: 11/19/2022]
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Rout PK, Kumar A, Mandal A, Laloe D, Singh SK, Roy R. Characterization of casein gene complex and genetic diversity analysis in Indian goats. Anim Biotechnol 2010; 21:122-34. [PMID: 20379889 DOI: 10.1080/10495390903534622] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Milk protein polymorphism plays an important role in genetic diversity analysis, phylogenetic studies, establishing geographical diversity, conservation decision, and improving breeding goals. Milk protein polymorphism in Indian goat breeds has not been well studied; therefore, an investigation was carried out to analyze the genetic structure of the casein gene and milk protein diversity at six milk protein loci in nine Indian goat breeds/genetic groups from varied agro-climatic zones. Milk protein genotyping was carried out in 1098 individual milk samples by SDS-PAGE at alphaS1-CN (CSN1S1), beta-CN (CSN2), alphaS2-CN (CSN1S2), kappa-CN (CSN3), beta-LG, and alpha-LA loci. Indian goats exhibited alphaS1-casein A allele in higher frequency in the majority of breeds except Ganjam and local goats. The alphaS1-casein A allele frequencies varied from 0.45 to 0.77. A total of 16 casein haplotypes were observed in seven breeds and breed specific haplotypes were observed with respect to geographic region. The average number of alleles was lowest in Ganjam (1.66 +/- 0.81) and highest in Sirohi goats (2.50 +/- 1.05). Expected heterozygosity at six different loci demonstrated genetic diversity and breed fragmentation. Neighbor-Joining tree was built basing on Nei's distance. There was about 16.95% variability due to differences between breeds, indicating a strong subdivision. Principal component analysis was carried out to highlight the relationship among breeds. The variability among goat breeds was contributed by alphaS2-CN, beta-LG and alphaS1-CN. The Indian goats exhibited alphaS1-CN (CSN1S1) A allele in higher frequency in all the breeds indicating the higher casein yield in their milk.
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Affiliation(s)
- P K Rout
- Central Institute for Research on Goats, Makhdoom, Farah, Mathura, India.
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47
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Giambra I, Jäger S, Erhardt G. Isoelectric focusing reveals additional casein variants in German sheep breeds. Small Rumin Res 2010. [DOI: 10.1016/j.smallrumres.2009.12.025] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Caroli A, Rizzi R, Lühken G, Erhardt G. Short communication: Milk protein genetic variation and casein haplotype structure in the Original Pinzgauer cattle. J Dairy Sci 2010; 93:1260-5. [DOI: 10.3168/jds.2009-2521] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2009] [Accepted: 11/09/2009] [Indexed: 11/19/2022]
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Caroli AM, Chessa S, Erhardt GJ. Invited review: milk protein polymorphisms in cattle: effect on animal breeding and human nutrition. J Dairy Sci 2010; 92:5335-52. [PMID: 19841193 DOI: 10.3168/jds.2009-2461] [Citation(s) in RCA: 279] [Impact Index Per Article: 19.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
The 6 main milk proteins in cattle are encoded by highly polymorphic genes characterized by several nonsynonymous and synonymous mutations, with up to 47 protein variants identified. Such an extensive variation was used for linkage analysis with the description of the casein cluster more than 30 yr ago and has been applied to animal breeding for several years. Casein haplotype effects on productive traits have been investigated considering information on the whole casein complex. Moreover, mutations within the noncoding sequences have been shown to affect the specific protein expression and, as a consequence, milk composition and cheesemaking. Milk protein variants are also a useful tool for breed characterization, diversity, and phylogenetic studies. In addition, they are involved in various aspects of human nutrition. First, the occurrence of alleles associated with a reduced content of different caseins might be exploited for the production of milk with particular nutritional qualities; that is, hypoallergenic milk. On the other hand, the frequency of these alleles can be decreased by selection of sires using simple DNA tests, thereby increasing the casein content in milk used for cheesemaking. Furthermore, the biological activity of peptides released from milk protein digestion can be affected by amino acid exchanges or deletions resulting from gene mutations. Finally, the gene-culture coevolution between cattle milk protein genes and human lactase genes, which has been recently highlighted, is impressive proof of the nonrandom occurrence of milk protein genetic variation over the centuries.
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Affiliation(s)
- A M Caroli
- Dipartimento di Scienze Biomediche e Biotecnologie, Università degli Studi di Brescia, Viale Europa 11, Brescia 25123, Italy.
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Sztankóová Z, Mátlová V, Kyseľová J, Jandurová O, Říha J, Senese C. Short communication: Polymorphism of casein cluster genes in Czech local goat breeds. J Dairy Sci 2009; 92:6197-201. [DOI: 10.3168/jds.2008-1519] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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