Table 1.

Significant SNPs (Bonferroni adjusted P < 0.05) associated with the mutant increased height phenotype

Scaffolda		SNP	P value	BSA Rankb	Effect	Gene		Positione
ID	bp					IDc	Descriptiond	Chr	Mbp
IWGSC_CSS_3B_scaff_						Traes_3B_
10394995	2370	G → A	1.4 × 10−5	8	G160S	9FD27C382	Dirigent protein 22-like [B. distachyon]	3B	779.1
10351351	3767	G → A	3.3 × 10−5	14	Synonymous	0B45CE6A2	n/a	3B	783.5
IWGSC_CSS_4AL_scaff_						Traes_4AL_
7173690	939	G → A	6.2 × 10−6	54	Intergenic			4A	645.1
7089505	1281	C → T	1.4 × 10−5	120	E254K	343B5D587	ATP-binding protein, putative [M. truncatula]	4A	674.3
7160166	4006	G → A	1.0 × 10−5	18	Intron	590B5CC39	Putative cysteine synthase [O. sativa]	4A	675.6
7100865	4872	C → T	2.0 × 10−5	42	Synonymous	A710BA481	RNA 2′-phosphotransferase, Tpt1/KptA family [A. thaliana]	4A	687.3
7070109	15,757	G → A	3.1 × 10−6	n/a	Q187*	71E0C196D	n/a	4A	689.0
7070109	30,790	C → T	1.7 × 10−5	n/a	W64*	760AA1408	n/a	4A	689.0
IWGSC_CSS_4BS_scaff_						Traes_4BS_
4920499	9117	G → A	5.8 × 10−6	12	R74Q	5A606CB40	Type I inositol-1,4,5-trisphosphate 5-phosphatase CVP2 [A. tauschii]	4B	12.5
4933555	4037	G → A	8.8 × 10−7	23	Synonymous	5AC244927	Endo-1,4-beta-xylanase C [A. tauschii]	4B	15.7
1070968	1979	C → T	8.8 × 10−7	15	Intergenic			4B	16.7
4872575	19,299	C → T	7.4 × 10−7	7	G359R	32B866B33	GDSL esterase/lipase [A. tauschii]	4B	20.6
4909391	8166	A → G	3.6 × 10−6	5	Intergenic			4B	20.7
4961119	20,843	G → A	1.7 × 10−6	4	Intron	F96B8575F	Plant/T23J7-180 protein, putative [M. truncatula]	4B	24.5
4963368	3342	G → A	1.6 × 10 −11	3	V604M	63DD9D036	Lipoxygenase 1 [A. tauschii]	4B	27.2
4884290	6797	C → T	1.1 × 10 −14	2	Intergenic			4B	27.5
4881784	3986	C → T	< 2.0 × 10 −16	1	Synonymous	ACBE893D5	Phytanoyl-CoA dioxygenase (PhyH) family protein [A. thaliana]	4B	31.7
4911525	11,750	C → T	4.8 × 10−6	6	5′ UTR	372652643	Maf-like protein [A. tauschii]	4B	45.2
4868930	6350	C → T	2.7 × 10−7	22	Synonymous	34AF89ACE	Transcription factor bHLH25 [A. tauschii]	4B	46.2
2307753	3238	C → T	2.4 × 10−6	20	Intron	A53F8B91F	Alpha/beta-Hydrolases superfamily protein [A. thaliana]	4B	47.6
4935065	7502	C → T	1.1 × 10−5	32	Intron	D4D9B5E3E	Sucrose-phosphate synthase family protein [A. thaliana]	4B	93.8
4904809	9422	G → A	3.3 × 10−5	39	G133R	BE761A604	Cysteine-rich receptor-like protein kinase 40 [T. urartu]	4B	95.3
IWGSC_CSS_5AL_scaff_						Traes_5AL_
2796973	5466	G → A	1.6 × 10−8	85	3′ UTR	2292EE446	Inositol 1,3,4-trisphosphate 5/6-kinase 4 [A. thaliana]	5A	514.2
2808395	209	C → T	3.1 × 10−7	107	L35F	EE0639A2E	Flap endonuclease GEN-like protein 1 [A. tauschii]	5A	522.1
IWGSC_CSS_6BL_scaff_						Traes_6BL_
4217811	4606	C → T	2.8 × 10−5	58	V13I	116641644	Calcium-binding EF hand family protein [A. trichopoda]	6B	449.8

The three most significant SNPs are in Bold

^aIWGSC CSS wheat survey sequence version 1

^bRank of each SNP ordered by |Δ(SNP-index)| in the BSA simulation (see Fig. 5)

^cPGSB/MIPS version 2.2

^dAnnotations from orthologues available at Ensembl Plants (http://archive.plants.ensembl.org/index.html). n/a signifies no annotated orthologous gene

^eIWGSC RefSeq v1.0