Table 2.

Favorable alleles observed in significant SNP positions (−log₁₀ p-value ≥ 5) on Chromosome 2 for phenotypic scores, using two GBS methods.

Position	GBS Method	Alleles	Tolerant		Intolerant
			Favorable Allele	No. of Accessions	Favorable Allele	No. of Accessions
392,560,939	tGBS	A/G	A	28	G	34
392,619,081	tGBS	C/G	C	26	G	35
392,619,090	tGBS	C/T	T	26	C	35
392,619,094	tGBS	A/T	A	26	T	35
392,619,099	tGBS	A/G	A	26	G	35
392,619,165	tGBS	A/C	C	28	A	35
392,690,695	tGBS	C/T	T	25	C	33
392,690,695	GBS-t	C/T	T	31	C	27
392,690,876	GBS-t	A/G	G	31	A	29
392,692,372	GBS-t	T/G	G	31	T	31
392,692,397	GBS-t	A/G	G	29	A	32
392,695,004	GBS-t	A/G	G	31	A	29
392,695,044	GBS-t	C/T	T	32	C	32
392,695,091	tGBS	A/G	A	23	G	35
392,695,091	GBS-t	A/G	A	32	G	32
392,695,192	tGBS	C/T	T	23	C	35
392,697,101	GBS-t	T/C	C	32	T	32
392,697,852	GBS-t	T/A	A	30	T	32
392,697,951	GBS-t	T/C	C	29	T	32
392,699,727	GBS-t	T/C	C	32	T	31
392,700,661	GBS-t	C/A	A	31	C	31
392,758,269	tGBS	C/T	C	26	T	33
392,767,939	GBS-t	C/A	A	28	C	30
393,426,328	tGBS	G/T	T	26	G	35
393,426,332	tGBS	C/T	T	22	C	35
393,427,373	GBS-t	C/T	T	31	C	30