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

Alfredo Pauciullo,Liliana Di Stasio,Gianfranco Cosenza,El Tahir Shuiep,Georg Erhardt,Moses Danlami Ogah

doi:10.3389/fgene.2019.00748

Alfredo Pauciullo, Liliana Di Stasio + Show 4 more

Open Access

https://doi.org/10.3389/fgene.2019.00748

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Abstract

The structure of casein genes has been fully understood in llamas, whereas in other camelids, this information is still incomplete. In fact, structure and polymorphisms have been identified in three (CSN1S1, αs1-CN; CSN2, β-CN; CSN3, κ-CN) out of four casein genes, whereas controversial information is available for the CSN1S2 (αs2-CN) in terms of structure and genetic diversity. Data from the genome analysis, whose assembly is available for feral camel, Bactrian, dromedary, and alpaca, can contribute to a better knowledge. However, a majority of the scaffolds available in GenBank are still unplaced, and the comparative annotation is often inaccurate or lacking.Therefore, the aims of this study are 1) to perform a comparative genome analysis and synthesize the literature data on camelids casein cluster; 2) to analyze the casein variability in two dromedary populations (Sudanese and Nigerian) using polymorphisms at CSN1S1 (c.150G > T), CSN2 (g.2126A > G), and CSN3 (g.1029T > C); and 3) to physically map the casein cluster in alpaca. Exon structures, gene and intergenic distances, large insertion/deletion events, SNPs, and microsatellites were annotated. In all camelids, the CSN1S2 consists of 17 exons, confirming the structure of llama CSN1S2 gene. The comparative analysis of the complete casein cluster (∼190kb) shows 12,818 polymorphisms. The most polymorphic gene is the CSN1S1 (99 SNPs in Bactrian vs. 248 in dromedary vs. 626 in alpaca). The less polymorphic is the CSN3 in the Bactrian (22 SNPs) and alpaca (301 SNPs), whereas it is the CSN1S2 in dromedary (79 SNPs). In the two investigated dromedary populations, the allele frequencies for the three markers are slightly different: the allele C at CSN1S1 is very rare in Nigerian (0.054) and Sudanese dromedaries (0.094), whereas the frequency of the allele G at CSN2 is almost inverted. Haplotype analysis evidenced GAC as the most frequent (0.288) and TGC as the rarest (0.005). The analysis of R-banding metaphases hybridized with specific probes mapped the casein genes on chromosome 2q21 in alpaca. These data deepen the information on the structure of the casein cluster in camelids and add knowledge on the cytogenetic map and haplotype variability.

Highlights

Camelids are the only living animals naturally spread over three continents: Africa, Asia, and South America
The organization and the orientation of the genes are highly conserved compared to all species studied to date, with large differences in sizes partially due to a diverse number and natures of the interspersed repeated elements [short interspersed elements (SINEs), long interspersed elements (LINEs), microRNA, etc.], partially due to genome expansion events and a higher number of genes present (Figure 1)
The ODAM gene was found, whereas no other known genes were found in the intergenic intervals CSN1S1-CSN2 and CSN2-CSN1S2

Summary

Introduction

Camelids are the only living animals naturally spread over three continents: Africa (dromedaries), Asia (dromedaries and both wild and domesticated Bactrians), and South America (llamas, alpacas, vicunas, and guanacos). These populations are not indigenous, but imported from middle of 1800 in Australia (McKnight, 1969), and more recently in Europe Since their domestication, Old and New world camelids have been exploited as multi-purpose animals for transportation (as beasts of burden), food (as source of milk and meat), and kept for their fiber (wool and hair), and for entertainment (as riding animals). Old and New world camelids have been exploited as multi-purpose animals for transportation (as beasts of burden), food (as source of milk and meat), and kept for their fiber (wool and hair), and for entertainment (as riding animals) These animals are of major economic and cultural importance for nomadic societies of Africa and Asia, as well as for the rural populations of South America. In the countries of the Gulf, intensive dromedary camel milk production in high-scale modernized unit has been already realized (Faye et al, 2002) and genetic improvement programs for the milk production have been implemented (Nagy et al, 2012)

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