Capture Sequencing to Explore and Map Rare Casein Variants in Goats

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.

FIGURE 1

Overview of the genetic variant types occurring within the four casein genes CSN1S1, CSN1S2, CSN2, and CSN3.

FIGURE 2

Amino acid sequence alignments of all casein protein variants detected in this study. (A) Alpha S1 casein, (B) beta casein, (C) alpha S2 casein, and (D) kappa casein. The reference protein variants were obtained from GenBank (CSN1S1: XP_017904616, 214 amino acids; CSN2: XP_005681778, 257 amino acids; CSN1S2: XP_013820127, 223 amino acids; CSN3: NP_001272516, 192 amino acids). The amino acid sequences for the casein variants were aligned and compared with the reference sequences using the multiple sequence alignment in Clustal Omega (http://www.ebi.ac.uk/Tools/msa/). The signal peptide sequences are labeled in gray, the mature protein sequences in black, and the amino acid differences are in bold. The positions of the amino acid substitutions in the mature protein are shown above the sequence. Asterisk indicates the same amino acids at the given position. Colon indicates conservation between groups of strongly similar properties—scoring >0.5 in the Gonnet PAM 250 matrix and both amino acids are similar to each other with respect to biological function. Dot indicates conservation between groups of weakly similar properties—scoring ≤0.5 in the Gonnet PAM 250 matrix.