Characterization of the OmyY1 Region on the Rainbow Trout Y Chromosome

Table 3

Primer information for markers in the OmyY1 BAC contig (#6256).The parental lines are the doubled haploid male (AR/SW) and female (OSU/WR) rainbow trout clonal lines in which the products were amplified. Clonal lines listed on either side of “/” denote which clonal lines have the SNP or indel. The last column shows the base pair location of the SNP(s) or indel in the amplified product.

Mapping primers	Gene	Primer name	Tm	BAC clone	Product size	Parental line	SNP or indel
F1:GCCTATCAACCTCCTGTACTT; R1:CCTGCGAAATAACCAATG	Fbxw2	Fbxw2-F/R	58–60	450D22/492A1	703 bp	AR, SW/OSU, WR	261bp
F2:CTACAGGAAGTCCAAACGAGG; R2:TGGGGATGGTAGTTGACAGTC	Fbxw2	Fbxw2-F2/R2	58–64	450D22/492A21	740 bp	AR, SW/OSU, WR	162(A/G); 525(T/A)
F3:TAGACATTTCCCCTGTATTACC; R3:AAAAGGGTCTGCTACTCATT	Fbxw2	Fbxw2-F3/R3	58	450D22/492A21	818 bp	AR, SW/OSU, WR	378(G/T), 530(G/C); 756(G/A), 642–46 bp
F4:CATGTCTTCTTTCCATTGGCC; R4:TTGTGACCTCCATCTTGTAGG	Intergenic	c451-grp2-F/R	62	450D22	392 bp	AR, SW/OSU, WR	147(G/T), 166(G/T)
F5:CGACAGCACCAAACTAATCTTT; R5:GATCATCAGTTGCACGGAGG	Intergenic	c35-450D22-F2-R2	62	450D22	978 bp	AR, SW/OSU, WR	male-specific; amplification
F6:TTACAGTGACATTCGGTTCAA; R6:TTTGGGTGTGTGATGCTATTT	Intergenic	MM121C-5′14kb	62	450D22/492A21	687 bp	AR/SW/OSU/WR	168(G/A)
F7:CGGAATGCACCAAACCCTAA; R7:GTATGTTGTCCTTGGCTCCGAA	Intergenic	1M42E-14201-; F5/14944-R	65	423A24	743 bp	AR/OSU	AFLP in AR