Table 4.

Validation of SNPs in candidate genes.

B.napus gene	Gene coordinates	Trait associated in GWAS	FDR adjusted p-value	Annotation	Functional category	SNPs	SNPs position (Darmor v4)	Allele	SNP effect	Confirmed	Indels	Type	Position
BnaA05g 23520	17777418–17781394	C18:1 C18:2	0.415746, 0.344113	AAE13	Lipid metabolism	UQSNP0001565	17777977	G/T	Missense variant	Confirmed	No
BnaA05g 23670	17875337–17876795			FAD5	Lipid metabolism	UQSNP0001629	17876056	A/C	Synonymous variant	Amplified area did not cover SNP area	No
						UQSNP0001630	17876071	T/C
BnaA05g 23930	18017224–18019348	C18:1 C18:2	0.415746, 0.344113	PPR-like	Transcription	UQSNP0001759	18018284	G/C	Missense variant	Amplified area did not cover SNP area
BnaA05g 24090	18138518–18143531		0.344113	WD40	Signal transduction	UQSNP0001827	18140199	C/G	Missense variant	Primers not specific
BnaA05g 23740	17921857–17925521			PLDALPHA1	Lipid metabolism	UQSNP0001673	17922271	C/T	Missense variant	Confirmed	Yes	AT (insertion)	17922566
						UQSNP0001674	17923336	C/A	Synonymous variant	Confirmed		AGATTTGCTTTTCTTTTTAAAT (deletion)	17922836
						UQSNP0001675	17923519	T/G	Synonymous variant
						UQSNP0001676	17923566	A/G	Synonymous variant
						UQSNP0001677	17923726	A/G	Synonymous variant	Amplified area did not cover SNP area
						UQSNP0001678	17924395	G/A	Synonymous variant
						UQSNP0001679	17924465	G/T	Missense variant
BnaA05g 23110	17520545–17528123			PLDP1	Lipid metabolism	UQSNP0001374	17521025	A/G	Missense variant	Confirmed		TTTAATTCT (deletion)	175520708
												AATATATAAGGTTATGATC (insertion)	17520803
						UQSNP0001377	17521925	A/G	Synonymous variant	No-Amplified area did not cover SNP area
						UQSNP0001383	17523040	T/C
						UQSNP0001384	17525851	C/A
						UQSNP0001386	17526546	A/G