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Table 1 Polymorphisms in SAD1, SAD2, FAD2A, FAD3A, and FAD3B genes associated with the fatty acid composition of flax oil

From: Genetic diversity of SAD and FAD genes responsible for the fatty acid composition in flax cultivars and lines

Site* Location Ref.
allele
Alt.
allele
Fatty
acid**
VarScan freeBayes
rs p-value rs p-value
SAD1 (Chr. CP027620.1)
2257330 Upstream A G OLE 0.37 4 × 10− 4 0.37 5 × 10− 4
2257353 Upstream T C OLE 0.35 0.001 0.33 0.002
2258938 Intron C G OLE 0.27 0.01 0.34 0.002
2258980 Intron T C OLE 0.34 0.002 0.37 6 × 10−4
2260202 Downstream T G OLE 0.35 0.001 0.32 0.003
SAD2 (Chr. CP027621.1)
17364707 Upstream A AG OLE 0.31 0.004 0.30 0.005
17365164 Exon T C STE 0.31 0.009 0.31 0.009
17367383 Downstream G T LIO −0.28 0.01 −0.28 0.01
FAD2A (Chr. CP027619.1)
5296364 Exon G A PAL −0.28 0.01 − 0.29 0.007
5296364 Exon G A STE −0.34 0.002 −0.34 0.002
5296658 Exon C T STE 0.38 4 × 10−4 0.39 3 × 10−4
5296705 Downstream C A PAL 0.35 0.006 0.35 0.005
FAD3A (Chr. CP027631.1)
16092241 Intron T C LIN −0.32 0.003 −0.35 0.001
16092241 Intron T C PAL 0.29 0.008 0.28 0.009
16092273 Intron C A LIN −0.32 0.003 −0.37 4 × 10−4
16092294 Exon T C LIN −0.33 0.002 −0.39 2 × 10− 4
16092294 Exon T C LIO 0.32 0.003 0.34 0.002
16092294 Exon T C PAL 0.36 7 × 10−4 0.35 0.001
16092348 Exon C T LIN −0.29 0.008 −0.29 0.007
16092348 Exon C T PAL 0.33 0.002 0.34 0.002
16092575 Exon C T LIN −0.36 8 × 10−4 −0.42 7 × 10−6
16092674 Upstream G T LIN −0.32 0.003 −0.38 3 × 10−4
16092741 Upstream T TAA LIN −0.37 5 × 10−4 − 0.36 8 × 10− 4
16093029 Upstream T C LIN −0.36 8 × 10−4 − 0.42 9 × 10− 6
16093029 Upstream T C LIO 0.27 0.01 0.28 0.01
16093029 Upstream T C PAL 0.39 3 × 10−4 0.40 2 × 10− 4
16093040 Upstream C A LIN −0.43 7 × 10−6 − 0.45 2 × 10− 6
16093040 Upstream C A LIO 0.33 0.003 0.29 0.008
16093040 Upstream C A PAL 0.35 0.001 0.33 0.002
FAD3B (Chr. CP027622.1)
1034358 Upstream G A STE 0.28 0.01 0.26 0.02
1034389 Upstream A G LIO −0.31 0.005 −0.31 0.004
1034526 Upstream C A LIO −0.26 0.02 −0.25 0.02
1034873 Upstream G A LIO −0.32 0.004 −0.27 0.02
1034904 Upstream G C LIO −0.30 0.007 −0.30 0.006
1035028 Upstream A G LIO −0.28 0.01 −0.29 0.007
1035480 Exon A G LIO −0.29 0.007 −0.30 0.006
1035655 Exon C T LIO 0.28 0.009 0.32 0.003
1035655 Exon C T LIN −0.37 6 × 10−4 −0.38 4 × 10−4
1035655 Exon C T PAL 0.32 0.003 0.33 0.002
1035674 Exon T G LIO −0.26 0.02 −0.29 0.007
1036195 Intron G T LIO −0.26 0.02 −0.30 0.006
1037964 Intron G C LIN −0.26 0.02 −0.25 0.02
  1. Ref. allele Reference allele, Alt. allele Alternative allele, PAL Palmitic acid, STE Stearic acid, OLE Oleic acid, LIO Linoleic acid, LIN Linolenic acid, rs – Spearman’s rank correlation coefficient between the ratio of Alt. allele and the content of fatty acid. Polymorphisms with rs < −0.25 or rs > 0.25 for both VarScan and freeBayes results are presented. The key polymorphisms in FAD3A and FAD3B genes associated with LIN content in flax oil are shown in bold. * – the coordinates are given according to the L. usitatissimum genome assembly GCA_000224295.2/ASM22429v2. ** – fatty acid with the content of which the polymorphism is associated