Table 1. SNPs with significant (P value<0.0001 and FDR P value<0.05) allele frequency differences in generation 8 between Low and High RFI selection lines.

SSC	SNP	Location of SNP	P value before FDR	−log P value	P Value after FDR	Genes within 0.5 Mb upstream of the SNP	Genes within 0.5 Mb downstream of the SNP
13	ASGA0060074	211966700	5.25E-08	7.27	0.002	SNORA72	KCNJ15
7	ASGA0030976	7981110	9.24E-08	7.03	0.002	TFAP2A, GCNT2, MAK, C6ORF52, TMEMB14	ELOVL2, NEDD9,
7	ALGA0043495	95603020	2.33E-07	6.63	0.003	GPX2, MAX, FNTB, CHURC1, SPTB, PLEKHG3, RAB15	FUT8
5	MARC0013717	63387978	9.94E-07	6.00	0.012	ETV6, SNORA22, 5srRNA	TCTP, LRP6, BCL-G, Novel transcript
7	H3GA0019660	5155195	2.24E-06	5.64	0.022	SSR1, RIOK1, DSP, SNRNP48	BMP6, EEF1E1, MUTED, LOC100515671
6	ALGA0122972	8687182	5.30E-06	5.27	0.038	No annotated genes	5s-rRNA, CLEC-34A, WWOX
3	ALGA0114825	79728805	5.30E-06	5.27	0.04	MEIS1	No annotated genes
13	MARC0069512	123984019	7.21E-06	5.14	0.04	No annotated genes	TBL1XR1, LOC100523210