Table 2.

Amino acid polymorphisms in candidate genes ELF3, GRIK1-like, and PWWP1 between cultivated T. monococcum ssp. monococcum accession DV92 carrying the Eps-A ^m 1-l allele for late heading, and wild T. monococcum ssp. aegilopoides accession G3116 carrying the Eps-A ^m 1-e allele for early heading. Amino acid changes are described indicating the ancestral amino acid first, followed by the position of that amino acid from the initial methionine in the T. urartu (PI 428198) protein, and the derived amino acid at the end. Ancestral and derived states are inferred from other grasses listed in Supplementary Table S8. PROVEAN, PolyPhen, and BLOSUM62 scores were estimated for the change from the ancestral to the derived variant. Scores predicting a disruptive effect on protein structure and function are indicated in italics

Gene	Amino acid change	DV92 allele	G3116 allele	PROVEANa	PolyPhen-2b	BLOSUM62c
ELF3	V364L	L	V	−0.688	0.574	1
	G681R	R	G	−2.781	0.116	−2
	G700D	G	D	1.046	0.999	−1
	G718A	G	A	0.613	0.114	0
GRIK1-like	D77E	D	E	0.389	0.012	2
	A228S	A	S	0.298	0.048	1
	D351N	D	N	−0.039	0.016	1
PWWP1	S251W	S	W	−2.023	0.992	−3
	T294M	M	T	0.653	0.050	−1
	S327I	S	I	−1.703	0.827	−2
	G542C	G	C	−0.540	0.999	−3
	V701A	A	V	0.387	0.455	0

^aPROVEAN scores were calculated at provean.jcvi.org. Scores <−2.5 are predicted to have a strong effect on protein function

^bPolylPhen-2 scores were calculated using genetics.bwh.harvard.edu/pph2/. Values close to 0 suggest limited effects on protein function, and values closer to 1 suggest more significant effects on protein structure and function

^cBLOSUM62 scores were obtained from BLOSUM62 substitution matrix (Henikoff and Henikoff 1992). The more negative the BLOSUM62 scores are, the higher is the probability of that amino acid change to disrupt protein structure or function