TABLE 2.
Allele frequency of non-synonymous variants in different goat breeds.
| Casein genes | CHR positiona | SNP IDb | Allele | Exon (nt position)c | Amino acid | Amino acid position in whole proteind | Amino acid position in mature protein | Frequency of alternative allele | |||||||
| NU (n = 7) | D (n = 5) | NI (n = 7) | Tagg (n = 7) | SA (n = 2) | Bez ibex (n = 2) | Nu ibex (n = 2) | Alp ibex (n = 1) | ||||||||
| CSN1S1 | 6:85981710 6:85981711 | rs268293069 rs655973384 | CA/AT | 3 (16/17) | His/Ile | 23 | 8 | 0 | 0 | 0 | 0 | 0.25 | 0 | 0 | 0 |
| 6:85982615 | rs155505532 | T/C | 4 (8) | Leu/Pro | 31 | 16 | 0.57 | 0.50 | 0.57 | 0.64 | 1.00 | 0 | 0 | 0 | |
| 6:85984154 | ss7213522403 | A/G | 7 (4) | Ile/Val | 59 | 44 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0.50 | |
| 6:85987197 | rs155505536 | C/G | 10 (21) | Gln/Glu | 92 | 77 | 0.57 | 0.50 | 0.57 | 0.64 | 1.00 | 0.50 | 0 | 0 | |
| 6:85988705 | rs268293072 | G/A | 12 (14) | Arg/Lys | 115 | 100 | 0.57 | 0.50 | 0.57 | 0.64 | 0.75 | 0.50 | 0 | 0 | |
| CSN2 | 6:86015278 | ss7213522526 | G/C | 1 (62) | Leu/Val | 11 | – | 0 | 0 | 0 | 0 | 0 | 0 | 0.25 | 1.00 |
| 6:86015259 | ss7213522558 | T/C | 1 (43) | His/Arg | 17 | – | 0 | 0 | 0 | 0 | 0 | 0 | 0.25 | 1.00 | |
| 6:86013169 | rs652629715 | T/G | 2 (11) | Ile/Leu | 49 | – | 0.07 | 0.10 | 0 | 0 | 0.25 | 0.50 | 0.25 | 1.00 | |
| 6:86008103 | ss7213522487 | G/A | 7 (175) | Pro/Leu | 198 | 148 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 1.00 | |
| 6:86008016 | rs155505539 | A/G | 7 (89) | Val/Ala | 227 | 177 | 0.50 | 0.50 | 0.50 | 0.57 | 0.57 | 0.50 | 0 | 1.00 | |
| CSN1S2 | 6:86079098 | rs640625134 | T/C | 2 (23) | Phe/Ser | 4 | – | 0 | 0 | 0 | 0.07 | 0.50 | 0 | 0 | 0 |
| 6:86081790 | ss7213522477 | T/C | 4 (16) | Phe/Ser | 32 | 17 | 0 | 0 | 0 | 0 | 0 | 0 | 0.50 | 0 | |
| 6:86081887 | ss7213522549 | T/C | 5 (2) | Ile/Thr | 35 | 20 | 0 | 0 | 0 | 0 | 0 | 0 | 0.75 | 0 | |
| 6:86085160 | rs659163710 | G/C | 11 (106) | Ala/Pro | 134 | 119 | 1.00 | 0.90 | 1.00 | 1.00 | 1.00 | 1.00 | 1.00 | 1.00 | |
| 6:86085714 | rs665830654 | G/A | 12 (7) | Glu/Lys | 142 | 127 | 0.21 | 0.10 | 0 | 0 | 0 | 0 | 0.25 | 0 | |
| 6:86089407 | ss7213522575 | G/A | 16 (11) | Ser/Asn | 184 | 169 | 0 | 0 | 0 | 0 | 0 | 0 | 0.75 | 0 | |
| CSN3 | 6:86208927 | ss7213522604 | G/A | 4 (70) | Ser/Asn | 54 | 33 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 1.00 |
| 6:86208939 | ss7213522610 | G/C | 4 (82) | Ser/Thr | 58 | 37 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 1.00 | |
| 6:86208960 | rs268293109 | A/G | 4 (103) | Gln/Arg | 65 | 44 | 0 | 0 | 0 | 0.07 | 0.50 | 0 | 0 | 0 | |
| 6:86209097 | rs268293113 | G/A | 4 (240) | Asp/Asn | 111 | 90 | 0.14 | 0.10 | 0 | 0 | 0 | 0 | 0 | 0 | |
| 6:86209263 | rs651045868 | T/C | 4 (406) | Val/Ala | 166 | 145 | 0.14 | 0.10 | 0 | 0 | 0 | 0 | 0 | 0 | |
NU, Nubian; D, Desert; NI, Nilotic; Tagg, Taggar; SA, Saanen; Bez ibex, Bezoar ibex; NU ibex, Nubian ibex; Alp ibex, Alpine ibex. –, The amino acid change did not occur in the mature protein sequence. aCapra hircus autosome (CHR) position relative to reference sequences: accession no. NC_030813. brs, reference IDs for known SNPs are available from Ensembl (www.ensembl.org/); ss, new SNPs from our sequencing assigned by the European Variation Archive (EVA). cnt, nucleotide position in the exon. dPositions of the amino acids according to the reference protein sequence [CSN1S1 (XP_017904616: 214 amino acids in the whole protein, 199 amino acids in the mature protein); CSN2 (XP_005681778: 257 amino acids in the whole protein, 207 amino acids in the mature protein); CSN1S2 (XP_013820127.2: 223 amino acids in the whole protein, 208 amino acids in the mature protein); CSN3 (NP_001272516: 192 amino acids in the whole protein, 171 amino acids in the mature protein].