Capture Sequencing to Explore and Map Rare Casein Variants in Goats

Siham A Rahmatalla; Danny Arends; Ammar Said Ahmed; Lubna M A Hassan; Stefan Krebs; Monika Reissmann; Gudrun A Brockmann

doi:10.3389/fgene.2021.620253

Capture Sequencing to Explore and Map Rare Casein Variants in Goats

Front Genet. 2021 Feb 23:12:620253. doi: 10.3389/fgene.2021.620253. eCollection 2021.

Authors

Siham A Rahmatalla^{1

2}, Danny Arends¹, Ammar Said Ahmed¹, Lubna M A Hassan³, Stefan Krebs⁴, Monika Reissmann¹, Gudrun A Brockmann¹

Affiliations

¹ Animal Breeding Biology and Molecular Genetics, Albrecht Daniel Thaer-Institute of Agricultural and Horticultural Sciences, Humboldt University of Berlin, Berlin, Germany.
² Department of Dairy Production, Faculty of Animal Production, University of Khartoum, Khartoum North, Sudan.
³ Animal Resource Research Corporation, Wildlife Research Center, Federal Ministry of Livestock, Fisheries and Rangelands, Khartoum North, Sudan.
⁴ Labor für Funktionelle Genomanalyse, Genzentrum, Ludwig-Maximilians-Universität (LMU), Munich, Germany.

Abstract

Genetic variations in the four casein genes CSN1S1, CSN2, CSN1S2, and CSN3 have obtained substantial attention since they affect the milk protein yield, milk composition, cheese processing properties, and digestibility as well as tolerance in human nutrition. Furthermore, milk protein variants are used for breed characterization, biodiversity, and phylogenetic studies. The current study aimed at the identification of casein protein variants in five domestic goat breeds from Sudan (Nubian, Desert, Nilotic, Taggar, and Saanen) and three wild goat species [Capra aegagrus aegagrus (Bezoar ibex), Capra nubiana (Nubian ibex), and Capra ibex (Alpine ibex)]. High-density capture sequencing of 33 goats identified in total 22 non-synonymous and 13 synonymous single nucleotide polymorphisms (SNPs), of which nine non-synonymous and seven synonymous SNPs are new. In the CSN1S1 gene, the new non-synonymous SNP ss7213522403 segregated in Alpine ibex. In the CSN2 gene, the new non-synonymous SNPs ss7213522526, ss7213522558, and ss7213522487 were found exclusively in Nubian and Alpine ibex. In the CSN1S2 gene, the new non-synonymous SNPs ss7213522477, ss7213522549, and ss7213522575 were found in Nubian ibex only. In the CSN3 gene, the non-synonymous SNPs ss7213522604 and ss7213522610 were found in Alpine ibex. The identified DNA sequence variants led to the detection of nine new casein protein variants. New variants were detected for alpha S1 casein in Saanen goats (CSN1S1 ^∗C1), Bezoar ibex (CSN1S1 ^∗J), and Alpine ibex (CSN1S1 ^∗K), for beta and kappa caseins in Alpine ibex (CSN2 ^∗F and CSN3 ^∗X), and for alpha S2 casein in all domesticated and wild goats (CSN1S2 ^∗H), in Nubian and Desert goats (CSN1S2 ^∗I), or in Nubian ibex only (CSN1S2 ^∗J and CSN1S2 ^∗K). The results show that most novel SNPs and protein variants occur in the critically endangered Nubian ibex. This highlights the importance of the preservation of this endangered breed. Furthermore, we suggest validating and further characterizing the new casein protein variants.

Keywords: Alpine ibex; Bezoar ibex; Nubian ibex; Saanen; Sudanese goats; casein; genetic variation; polymorphism.