Casein Gene Cluster in Camelids: Comparative Genome Analysis and New Findings on Haplotype Variability and Physical Mapping

Pauciullo, Alfredo; Shuiep, El Tahir S.; Ogah, Moses Danlami; Cosenza, G.; Stasio, Liliana Di; Erhardt, G.

doi:10.3389/fgene.2019.00748

Cited by 13 publications

(32 citation statements)

References 85 publications

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“…All these caseins are encoded by autosomal genes CSN1S1, CSN2 , CSN1S2 , and CSN3 , respectively in closely linked DNA clusters ( Pauciullo et al, 2019 ). The genomic cluster of the casein gene spans between 250 and 350 kb in different mammalian species ( Ryskaliyeva, 2018 ), and in buffalo entire CSN gene covers a region of 250kb.…”

Section: Discussionmentioning

confidence: 99%

“…Further, the genomic sequences were analyzed in TFBIND software 8 by using the transcription factor database TRANSFAC R.3.4 weight matrix to find the transcription factor binding sites ( Tsunoda and Takagi, 1999 ). According described previously, four potential transcription factor binding sites (GATA, TATA, STAT, and OCT1) ( Hennighausen and Robinson, 1998 ; Robinson et al, 1998 ; Rosen et al, 1999 ; Wheeler et al, 2001 ; Wyszomierski and Rosen, 2001 ; Yamashita et al, 2001 ; Chughtai et al, 2002 ; Pauciullo et al, 2019 ) and one repressor site (YY1) ( Helman et al, 1998 ; Tomic et al, 1999 ) in casein genes of Mediterranean and swamp buffalo in 100bp upstream regions of the potential signal site were calculated ( Wyszomierski and Rosen, 2001 ). The significant difference for the distribution of putative transcription factor binding and repressor sites in Mediterranean and swamp buffalo was statistically evaluated by using a t -test with a P- value of < 0.05 as statistical significance.…”

Section: Methodsmentioning

confidence: 99%

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Comparative Genomics, Evolutionary and Gene Regulatory Regions Analysis of Casein Gene Family in Bubalus bubalis

Rehman

Tong-qing

et al. 2021

Front. Genet.

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Buffalo is a luxurious genetic resource with multiple utilities (as a dairy, draft, and meat animal) and economic significance in the tropical and subtropical regions of the globe. The excellent potential to survive and perform on marginal resources makes buffalo an important source for nutritious products, particularly milk and meat. This study was aimed to investigate the evolutionary relationship, physiochemical properties, and comparative genomic analysis of the casein gene family (CSN1S1, CSN2, CSN1S2, and CSN3) in river and swamp buffalo. Phylogenetic, gene structure, motif, and conserved domain analysis revealed the evolutionarily conserved nature of the casein genes in buffalo and other closely related species. Results indicated that casein proteins were unstable, hydrophilic, and thermostable, although αs1-CN, β-CN, and κ-CN exhibited acidic properties except for αs2-CN, which behaved slightly basic. Comparative analysis of amino acid sequences revealed greater variation in the river buffalo breeds than the swamp buffalo indicating the possible role of these variations in the regulation of milk traits in buffalo. Furthermore, we identified lower transcription activators STATs and higher repressor site YY1 distribution in swamp buffalo, revealing its association with lower expression of casein genes that might subsequently affect milk production. The role of the main motifs in controlling the expression of casein genes necessitates the need for functional studies to evaluate the effect of these elements on the regulation of casein gene function in buffalo.

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Section: Discussionmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Comparative Genomics, Evolutionary and Gene Regulatory Regions Analysis of Casein Gene Family in Bubalus bubalis

Rehman

Tong-qing

et al. 2021

Front. Genet.

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“…However, this is a relatively rare event. In fact, it is well-known that many recombination events characterise the casein cluster (Caroli et al 2009;Pauciullo et al 2019).…”

Section: Resultsmentioning

confidence: 99%

A novel duplex ACRS-PCR for composite CSN1S1–CSN3 genotype discrimination in domestic buffalo

Pauciullo

Martorello

Carku

et al. 2021

Italian Journal of Animal Science

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This short communication aimed to develop a fast and straightforward method for the simultaneous discrimination in buffaloes of the alleles CSN1S1 A/B and CSN3 X1/X2 using a single protocol. DNA was isolated from 219 individual blood samples. A duplex artificially created restriction site (ACRS-PCR) was accomplished using two pairs of primers generating 86 bp (CSN1S1) and 160 bp (CSN3). Amplicons were contemporary digested by MboI and HinfI for the identification of genotypes. The double simultaneous amplification and digestion proved to be effective for allele identification. The method resulted particularly quick due to the small PCR amplicons and fast digest enzymes that allowed both a rapid amplification (about 1 h and 40 min) and digestion in 10 min. Population analysis indicated that minor allele frequencies were CSN1S1 A (0.425) and CSN3 X2 (0.306). Linkage disequilibrium (LD) showed r 2 ¼0.46, and haplotype analysis revealed all four possible combinations with higher frequency for the CSN1S1 B-CSN3 X1 (0.553). Considering the tremendous economic impact of the CSN1S1-CSN3 variants on the dairy production in buffalo, this method, applicable immediately after the birth from any DNA source, may speed up the selection of sires and dams' lines with more favourable genotypes. HIGHLIGHTSCSN1S1-CSN3 composite genotype influences dairy performances. Duplex ACRS-PCR identifies the CSN1S1-CSN3 composite genotype in a single protocol. The duplex ACRS-PCR method may speed up the selection of lines with more favourable genotypes.

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“…Although many retroposons are common for the ruminants and non-ruminant species and, thus, are likely of ancestral origin, every species has a definite number of short interspersed nuclear elements, which contributes to make each genome specific for each species (Ramunno et al, 2004 ; Cosenza et al, 2005 ; Pauciullo et al, 2013 , 2019 ).…”

Section: Discussionmentioning

confidence: 99%

“…The accumulation of interspersed repeats within or near genes has been studied in ruminants as well as in camelid casein genes (Groenen et al, 1993 , Ramunno et al, 2004 , Cosenza et al, 2009b , Pauciullo et al, 2013 , 2014 , 2019 ). It has not been observed that insertions within or near promoters or 3′ UTR can alter gene expression.…”

Section: Discussionmentioning

confidence: 99%

Complete CSN1S2 Characterization, Novel Allele Identification and Association With Milk Fatty Acid Composition in River Buffalo

Cosenza¹,

Gallo²,

Auzino³

et al. 2021

Front. Genet.

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The αs2-casein is one of the phosphoproteins secreted in all ruminants' milk, and it is the most hydrophilic of all caseins. However, this important gene (CSN1S2) has not been characterized in detail in buffaloes with only two alleles detected (reported as alleles A and B), and no association studies with milk traits have been carried out unlike what has been achieved for other species of ruminants. In this study, we sequenced the whole gene of two Mediterranean river buffalo homozygotes for the presence/absence of the nucleotide C (g.7539G>C) realized at the donor splice site of exon 7 and, therefore, responsible for the skipping of the same exon at mRNA level (allele B). A high genetic variability was found all over the two sequenced CSN1S2 alleles. In particular, 74 polymorphic sites were found in introns, six in the promoter, and three SNPs in the coding region (g.11072C>T, g.12803A>T, and g.14067A>G) with two of them responsible for amino acid replacements. Considering this genetic diversity, those found in the database and the SNP at the donor splice site of exon 7, it is possible to deduce at least eight different alleles (CSN1S2 A, B, B1, B2, C, D, E, and F) responsible for seven different possible translations of the buffalo αs2-casein. Haplotype data analysis suggests an evolutionary pathway of buffalo CSN1S2 gene consistent with our proposal that the published allele CSN1S2 A is the ancestral αs2-CN form, and the B2 probably arises from interallelic recombination (single crossing) between the alleles D and B (or B1). The allele CSN1S2 C is of new identification, while CSN1S2 B, B1, and B2 are deleted alleles because all are characterized by the mutation g.7539G>C. Two SNPs (g.7539G>C and g.14067A>G) were genotyped in 747 Italian buffaloes, and major alleles had a relative frequency of 0.83 and 0.51, respectively. An association study between these SNPs and milk traits including fatty acid composition was carried out. The SNP g.14067A>G showed a significant association (P < 0.05) on the content of palmitic acid in buffalo milk, thus suggesting its use in marker-assisted selection programs aiming for the improvement of buffalo milk fatty acid composition.

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Casein Gene Cluster in Camelids: Comparative Genome Analysis and New Findings on Haplotype Variability and Physical Mapping

Cited by 13 publications

References 85 publications

Comparative Genomics, Evolutionary and Gene Regulatory Regions Analysis of Casein Gene Family in Bubalus bubalis

Comparative Genomics, Evolutionary and Gene Regulatory Regions Analysis of Casein Gene Family in Bubalus bubalis

A novel duplex ACRS-PCR for composite CSN1S1–CSN3 genotype discrimination in domestic buffalo

Complete CSN1S2 Characterization, Novel Allele Identification and Association With Milk Fatty Acid Composition in River Buffalo

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