Table 4.
Characterization of the three missense mutations identified in this study
| Features | Missense mutations identified as divergent variants based on the analysis of whole-genome sequence datasets from Churra and Australian Merino samples | |||
|---|---|---|---|---|
| SNP position (Oar_v3.1) | 52,429,848 | 37,308,727 | 37,3557,21 | 37,356,400 |
| Chromosome | 2 | 6 | 6 | 6 |
| dbSNP_ID | rs160159505 | rs159958168 | rs419074913 | rs159958380 |
| Gene | NPR2 | NCAPG | LCORL a | LCORL a |
| Ref. (Texel Oar_v3.1) → Altb | T → C | C → T | T → A | A → T |
| Position in CDS | c.2540 | c.1754 | c.4321c | c.3642c |
| Base pair substitution in CDS | T → C | C → T | A → T | T → A |
| Breed (mutant allele)d | Merino | Merino | Churra | Merino |
| Codon change | cAc → cGc | TCC → TTC | ATA → TTA | GAT → GAA |
| Amino acid change | Histitine (H) → Arginine (R) | Serine (S) → Phenilalanine (F) | Isoleucine (I) → Leucine (L) | Aspartate (D) → Glutamate (E) |
| Protein change | NPR2_His847Arg | NCAPG_Ser585Phe | LCORL_Ile1441Leu | LCORL_Asp1214Glu |
| Functional impact (ensemblVEP_Oarv3.1) | Moderate | Moderate | Moderate | Moderate |
| Functional impact (Polyphen-2) | Benign | Benign (score = 0.252; sensitivity: 0.91; specificity: 0.88) | Benign | Benign |
| Functional impact (SIFT_Oarv3.1) | Tolerated | Deleterious | Tolerated (low confidence) | Tolerated |
| Properties of wild aminoacid | Moderate hydropathy, charge “+” | Hydrophilic, polar, no charge | Hydrophobic, no charge | Hydrophilic, charge “−” |
| Properties of mutant aminoacid | Hydrophilic, charge “+” | Hydrophobic, apolar, no charge | Hydrophobic, no charge | Hydrophilic,, charge “−” |
| Churra genotypes | TT (15) | CC (14), CT (1) | AT (1), TT (14) | AA (14), AT (1) |
| Australian Merino genotypes | CC (9), TC (4) | TT (9), TC (3), CC (1) | AA (9), AT (3), TT (1) | TT (9), TA (3), AA (1) |
aMutation initially annotated within the ENSOARG00000004249 novel gene (Oar_3.1). BLASTN analyses showed correspondence with the human LCORL gene and the ovine LCOR according to the most recent version of the sheep genome (Oar_v4.0)
bRef. (Texel Oar_v3.1) → Alt: Reference and alternative alleles, respectively, identified in the analysis of the whole-genome sequence datasets
cPosition of the SNP in the coding sequence based on the alignment of the sequence harboring the mutation to the annotation of the LCORL gene in the most recent version of the sheep genome (Oar_v4.0): NCBI Reference sequences: XM_015096407.1, XP_014951893.1 (ligand-dependent nuclear receptor corepressor-like protein isoform X1)
dBreed with the highest frequency for the mutant allele (regarding the wild protein sequence). Note that for SNP rs419074913, the Texel sheep of the reference genome harbors the mutant allele according the CDS and protein sequence