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

Dmitriev, Alexey A.; Kezimana, Parfait; Rozhmina, Tatiana A.; Zhuchenko, Alexander A.; Povkhova, Liubov V.; Pushkova, Elena N.; Novakovskiy, Roman O.; Pavelek, Martin; Vladimirov, Gleb N.; Nikolaev, Evgeny N.; Kovaleva, Oxana A.; Kostyukevich, Yury I.; Chagovets, Vitaliy V.; Romanova, Elena V.; Snezhkina, Anastasiya V.; Kudryavtseva, Anna V.; Krasnov, George S.; Melnikova, Nataliya V.

doi:10.1186/s12870-020-02499-w

BMC Plant Biology

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
Site*	Location	Ref. allele	Alt. allele	Fatty acid**	r_s	*p-value*	r_s	*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

Ref. allele Reference allele, Alt. allele Alternative allele, PAL Palmitic acid, STE Stearic acid, OLE Oleic acid, LIO Linoleic acid, LIN Linolenic acid, r_s – Spearman’s rank correlation coefficient between the ratio of Alt. allele and the content of fatty acid. Polymorphisms with r_s < −0.25 or r_s > 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

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