Table 1 Loci analyzed, primers for amplicon sequencing, cDNA cloning and allele-specific amplification, annealing temperatures (Ta), amplicon sizes, and number of SNPs scored
Gene Acronym (GenBank Accession No.)Locus PGSC0003DMGChr.Primer Sequences 5′-3′ (* Primer Used for Amplicon Sequencing)Ta, °CAmplicon Size, bpNo. SNPs and Indels Scored
GWD (Y09533)400007677Vf-ATAAAAGTCAAAGCAAAGAAGAGCCT5777030
*r-GGATAATGCCCAGTGAAGAGTAAT
PWD (AY747068)400016613IX*f-GGTCTGATGATCTATCTGATTGC5787129
r-GACATCTTGAGGAGAACCAAACTT
BMY-8/2 (AF393847)400001855VIII*f-GCTACTGGA(Ino)CATGGTGACAGAa
r-TTACATAGAGGTCTGTCCTGCTTGAG5756014
PHO1b (StpL) (X73684)400028382Vf-TGTTGCAAGAAAAGCTAAACCAA57117838
*r-GATCACCAATCTCGGGATCA
SssI (Y10416)401018552IIIf-GGATACTCATGGGAAATAACAACTCC57102210
*r-CAATCAGGTCGAATTGGAAGG1 indel
PGM-3 (AJ240053)Not annotatedIII*f-ATGGCTATGGAGAGTGCATTGA57106015
r-GTATCCAATTGGCAAGGTAATTGTC
AGPaseS (X61187)400000735I*f-GGAGATGGATTTGTCGAGGT5693325
r-TGACCAGCCCAAAATCTGAT
INV-8/2 (NM_001247140)400004790VIII*f-GTTCTCATCCCACCACCCG56109615
r-CGTTCACCAGATCCACCACTC
PHO1a (Stp23) (X52385, D00520)Not annotatedIIIf-ATCACTCTCATTCGAAAAGCTAGAT652976-b
r-TGCCTTTGTTATTTTTCATTCACTTC
f-GCTAGATTTGCATAGAGAGCACA663031-b
r-GTGGTAATAACATCATCCTCTTACAC
*f-GAGGACCGAACACAACACACTT592100C22T
r-CACCTCCTCCTGACCATCTT
*f-GCGACCTGAGTTCTTTTGCT591400G322A
r-CATGCTTTGGTGTGCTCTCC
f-AGTTCTTTTGCTCCTGATGCC59–54 c-dG824
r-GAACATCATACGCAACTGTCC
f-TGAAATAAGGGAAGAGGTTGGA59–54 c-dA2776
r-AACAAACTGGACTTACTTTCTGATT
f-CTTAGAAAAGAAAGAGCTGGCA59–54c-dA2578
r-CAAAGTCAATAGCATACACAAAACAT
  • SNP, single-nucleotide polymorphism; PCR, polymerase chain reaction.

  • a Modified from (Krusiewicz et al. 2011)

  • b Primers for cDNA synthesis.

  • c Touch down PCR with ΔT° of −0.5°C.

  • d Primers for SNP allele specific amplification.