1
|
Vanvanhossou SFU, Giambra IJ, Yin T, Brügemann K, Dossa LH, König S. First DNA Sequencing in Beninese Indigenous Cattle Breeds Captures New Milk Protein Variants. Genes (Basel) 2021; 12:1702. [PMID: 34828308 PMCID: PMC8625544 DOI: 10.3390/genes12111702] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 10/22/2021] [Accepted: 10/25/2021] [Indexed: 11/16/2022] Open
Abstract
This study investigated polymorphisms in the milk protein genes CSN1S1, CSN2, CSN1S2, CSN3, LALBA, and LGB, and casein haplotypes in Beninese indigenous cattle. Considering 67 animals, DNA sequencing of the genes' exons, flanking regions and parts of the 5'-upstream regions identified 1058 genetic variants including 731 previously unknown. In addition, four novel milk protein variants were detected, including CSN3K (p.Ala66Val), LALBAF (p.Arg58Trp), LGBB1 (p.Ala134Val) and LGBK (p.Thr92Asnfs*13). CSN3K is caused by a novel SNP (BTA6:85656526C>T, exon 4) whereas LALBAF and LGBB1 are due to rs714688595C>T (exon 1) and rs109625649C>T (exon 4), respectively. Regarding LGBK, a frameshift insertion of one adenine residue at BTA11:103257980 (exon 3) induces a premature translation termination resulting in a 46% reduction of the reference protein sequence. The casein polymorphisms formed five main CSN1S1-CSN2-CSN1S2-CSN3 haplotypes including B-A1-A-B, B-A1-A-A and C-A2-A-B which are predominant in the investigated cattle breeds. Moreover, in silico analyses of polymorphisms within the 5'- and 3'- untranslated regions of all six milk proteins revealed effects on microRNA and transcription factor binding sites. This study suggests a large genetic variation of milk protein genes in Beninese cattle, which should be investigated in further studies for their effects on milk production, including quality and yield traits.
Collapse
Affiliation(s)
- Sèyi Fridaïus Ulrich Vanvanhossou
- Institute of Animal Breeding and Genetics, Justus-Liebig-University Gießen, 35390 Gießen, Germany; (S.F.U.V.); (I.J.G.); (T.Y.); (K.B.)
| | - Isabella Jasmin Giambra
- Institute of Animal Breeding and Genetics, Justus-Liebig-University Gießen, 35390 Gießen, Germany; (S.F.U.V.); (I.J.G.); (T.Y.); (K.B.)
| | - Tong Yin
- Institute of Animal Breeding and Genetics, Justus-Liebig-University Gießen, 35390 Gießen, Germany; (S.F.U.V.); (I.J.G.); (T.Y.); (K.B.)
| | - Kerstin Brügemann
- Institute of Animal Breeding and Genetics, Justus-Liebig-University Gießen, 35390 Gießen, Germany; (S.F.U.V.); (I.J.G.); (T.Y.); (K.B.)
| | - Luc Hippolyte Dossa
- School of Science and Technics of Animal Production, Faculty of Agricultural Sciences, University of Abomey-Calavi, Abomey-Calavi, 03 BP 2819 Jéricho Cotonou, Benin;
| | - Sven König
- Institute of Animal Breeding and Genetics, Justus-Liebig-University Gießen, 35390 Gießen, Germany; (S.F.U.V.); (I.J.G.); (T.Y.); (K.B.)
| |
Collapse
|
2
|
Association between single nucleotide polymorphisms (SNPs) and milk production traits in Italian Brown cattle. Livest Sci 2013. [DOI: 10.1016/j.livsci.2013.07.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
3
|
da Silva AM, de Freitas MAR, Rios AFL, Renzi A, Lôbo RB, Galerani MAV, Vila RA, Ramos ES. Identification of a DNA methylation point in the promoter region of the bovine CYP21 gene. GENETICS AND MOLECULAR RESEARCH 2012; 10:1409-15. [PMID: 21823090 DOI: 10.4238/vol10-3gmr1266] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
The CYP21 (steroid 21-hydroxylase) gene is involved in the synthesis of steroid hormones. Bov-A2 is a retroposon that is common in ruminant genomes. The promoter region of bovine CYP21 contains a short interspersed nucleotide element of Bov-A2, which overlaps a putative Sp1 binding site. We looked for RFLP/HpaII polymorphism in the Bov-A2 element in bovine Zebu breeds by PCR-RFLP, and examined whether polymorphism in this element is associated with methylation. Among DNA samples from 135 Brazilian Zebu breed cattle, we identified an RFLP/HpaII polymorphism (T/C), which, based on a restriction methylation-sensitive assay employing HpaII and isoschizomer MspI enzymes (methylation-sensitive and -non-sensitive enzymes, respectively), appears to be a DNA methylation point. This is the first report of this polymorphism and on DNA methylation in the bovine CYP21 promoter region in Brazilian Zebu cattle.
Collapse
Affiliation(s)
- A M da Silva
- Departamento de Genética, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP, Brasil
| | | | | | | | | | | | | | | |
Collapse
|
4
|
An analysis of CYP19, CYP21 and ER genotypes in Polish Holstein-Friesian cows with regard to the selected reproductive traits. ACTA VET BRNO 2011. [DOI: 10.2754/avb201180010065] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The aim of this study was to relate polymorphic variants of CYP19, CYP21 and ER1 genes to reproductive traits in 472 Polish Holstein-Friesian cows. High frequencies of one of the homozygous genotypes were found. The ER1/SnaBIAA homozygotes were not identified. In the first and third lactation, an average calving-to-conception interval (CLVC) in cows of ER1/SnaBIGG genotype was significantly shorter (P ≤ 0.05) than in heterozygous cows. In the cows of ER1/BglIGG genotype, significantly shorter CLVC (P ≤ 0.05) was observed compared to heterozygotes in the first lactation, whereas in the third lactation, CLVC in homozygous cows was significantly longer (P ≤ 0.05) than in heterozygous ones. It was also found that homozygous cows were characterized by significantly longer calving interval (CLVI; P ≤ 0.05) compared to heterozygotes in the third lactation. Longer CLVCs in CYP19AA cows were found, compared to heterozygotes, and this difference was significant in the first and third lactation (P ≤ 0.05). Similarly, the average CLVIs were longer in CYP19AA homozygotes than in heterozygous cows; however, significance was proven only in the third lactation (P ≤ 0.05). Description of the molecular mechanisms regulating reproduction, and thus identification of the individuals of genotypes with optimal potential may facilitate the employment of selected reproductive model by a breeder.
Collapse
|
5
|
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.
Collapse
Affiliation(s)
- A M Caroli
- Dipartimento di Scienze Biomediche e Biotecnologie, Università degli Studi di Brescia, Viale Europa 11, Brescia 25123, Italy.
| | | | | |
Collapse
|
6
|
Onami JI, Nikaido M, Mannen H, Okada N. Genomic expansion of the Bov-A2 retroposon relating to phylogeny and breed management. Mamm Genome 2007; 18:187-96. [PMID: 17436038 DOI: 10.1007/s00335-007-9000-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2006] [Accepted: 12/21/2006] [Indexed: 10/23/2022]
Abstract
Bov-A2 is a retroposon that is widely distributed among the genomes of ruminants (e.g., cow, deer, giraffe, pronghorn, musk deer, and chevrotain). This retroposon is composed of two monomers, called Bov-A units, which are joined by a linker sequence. The structure and origin of Bov-A2 has been well characterized but a genome-level exploration of this retroposon has not been implemented. In this study we performed an extensive search for Bov-A2 using all available genome sequence data on Bos taurus. We found unique Bov-A2-derived sequences that were longer than Bov-A2 due to amplification of three to six Bov-A units arranged in tandem. Detailed analysis of these elongated Bov-A2-derived sequences revealed that they originated through unequal crossing-over of Bov-A2. We found a large number of these elongated Bov-A2-derived sequences in cattle genomes, indicating that unequal crossing-over of Bov-A2 occurred very frequently. We found that this type of elongation is not observed in wild bovine and is therefore specific to the domesticated cattle genome. Furthermore, at specific loci, the number of Bov-A units was also polymorphic between alleles, implying that the elongation of Bov-A units might have occurred very recently. For these reasons, we speculate that genomic instability in bovine genomes can lead to extensive unequal crossing-over of Bov-A2 and levels of polymorphism might be generated in part by repeated outbreeding.
Collapse
Affiliation(s)
- Jun-ichi Onami
- Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Yokohama, Japan
| | | | | | | |
Collapse
|
7
|
Chessa S, Chiatti F, Ceriotti G, Caroli A, Consolandi C, Pagnacco G, Castiglioni B. Development of a Single Nucleotide Polymorphism Genotyping Microarray Platform for the Identification of Bovine Milk Protein Genetic Polymorphisms. J Dairy Sci 2007; 90:451-64. [PMID: 17183114 DOI: 10.3168/jds.s0022-0302(07)72647-4] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
The objective of this study was to develop and validate a fast method for typing the main mutations of bovine milk protein genes by using microarray technology. An approach based on the ligation detection reaction (LDR) and a universal array (UA) was used. Polymorphisms in both the coding and noncoding sequences of alpha(S1)-casein, beta-casein, kappa-casein, and beta-lactoglobulin genes were considered because of their well-known effects on milk composition and cheese production. A total of 22 polymorphic sites, corresponding to 21 different variants, were included in the diagnostic microarray. First, a multiplex PCR was developed to amplify all the DNA target sequences simultaneously. Second, the LDR-UA assay was implemented. The method was validated by analyzing 100 Italian Friesian DNA samples, which were also genotyped by conventional methods both at the protein level by means of milk isoelectrofocusing and at the molecular level using PCR-RFLP and PCR-single strand conformation polymorphism techniques. The genotypes obtained using the LDR-UA approach were in full agreement with those obtained by the conventional analyses. An important result of the LDR-UA assay was a more accurate genotyping of the different milk protein alleles than was found with conventional typing methods. At the kappa-casein gene, in fact, 4 samples were heterozygous (3 reference samples and 1 validation sample) for an allele coding for Thr(136) and Ala(148). This variant, which can be considered as the wild type of the genus Bos, is not usually identifiable by the conventional typing methods used. The multiplex PCR-LDR-UA approach developed provides for an accurate, inexpensive, and high-throughput assay that does not exhibit false positive or false negative signals, thus making it highly suitable for animal genotyping.
Collapse
Affiliation(s)
- S Chessa
- Dipartimento di Scienze e Tecnologie Veterinarie per la Sicurezza Alimentare, Università degli Studi di Milano, Via Trentacoste 2, Milano 20134 Italy.
| | | | | | | | | | | | | |
Collapse
|
8
|
Boettcher PJ, Caroli A, Stella A, Chessa S, Budelli E, Canavesi F, Ghiroldi S, Pagnacco G. Effects of casein haplotypes on milk production traits in Italian Holstein and Brown Swiss cattle. J Dairy Sci 2005; 87:4311-7. [PMID: 15545395 DOI: 10.3168/jds.s0022-0302(04)73576-6] [Citation(s) in RCA: 80] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
The objective of this study was to estimate the effects of different haplotypes of the casein genes on milk production traits in Italian dairy cattle. Traits of interest were yields of milk, fat, and protein, and percentages of fat and protein in milk. The data included 728 multiparous records from 347 Holsteins and 773 records from 298 Brown Swiss cows. Records were preadjusted for effects of age and parity, season of calving, and region, and expressed as deviations from herdmate averages. Twenty half-sib families were represented in each breed. Haplotype probabilities were estimated for each animal and phenotypes were regressed on these probabilities. Nine haplotypes were observed in Holsteins and 17 were identified among the Brown Swiss. For Holsteins, significant effects were observed for protein percentage, with some indication of an effect for fat percentage. For the Brown Swiss, effects of haplotypes were significant for milk yield and fat and protein percentages. Effects were strongest for protein percentage. Correlation coefficients of solutions across breeds tended to be strong and positive, indicating that the same haplotypes had similar estimated effects in the 2 breeds. Although the data were limited (<350 cows in each study), this latter result may suggest that genes in the casein complex itself are responsible for the effects observed, rather than loci that are physically linked on either side of the casein cluster.
Collapse
Affiliation(s)
- P J Boettcher
- Institute of Agricultural Biology and Biotechnology, National Research Council, Segrate 20090, Italy.
| | | | | | | | | | | | | | | |
Collapse
|