Characterisation of a transcriptome to find sequence differences between two differentially migrating subspecies of the willow warbler Phylloscopus trochilus

Table 4 Highly differentiated SNPs validated with Sanger sequencing

Gene name	Position in zebra finch genome	Min reads/pool	DI 454	DI Sanger S Sweden N Sweden/ S Sweden Lithuania
RNF6*	Chr1: 48,509,942	13	0.92	0.69/0.56
RB1*	Chr1: 56,558,186	9	1.00	0.81/0.50
ESD*	Chr1: 57,059,422	12	0.92	0.63/0.38
ESD*	Chr1: 57,059,472	11	0.91	0.75/0.43
XPOT	Chr1A: 32,952,256	10	0.94	0.19
ADCYAP1R1	Chr2: 3,348,189	8	0.92	0.00
RNMT	Chr2:101,951,215	13	0.93	0.19
RNMT	Chr2:101,951,219	12	0.92	0.13
BAI3	Chr3: 86,028,013	9	0.92	0.06
ENSTGUG00000005084*	Chr5: 3,850,065	18	0.91	0.88/0.88
FADS3*	Chr5: 6,375,371	30	0.95	0.88/0.94
FADS3*	Chr5: 6,375,565	25	0.96	0.94/0.94
FADS3*	Chr5: 6,375,583	22	0.96	0.75/0.69
SORD	Chr10: 3,477,546	15	0.94	0.00

Of the 14 candidate SNPs identified by the transcriptome analyses, eight ^(*) showed high to moderate differentiation (DI > 0.6) between southern (N = 8) and northern Swedish samples (N = 8) when independently validated by Sanger sequencing. These eight SNPs also showed elevated DIs between southern Swedish and Lithuanian samples (N = 8). The SNP in ADCYAP1R1 could only be successfully genotyped in four southern and five northern Swedish samples in the validation set.

ISSN: 1471-2164