Supplementary Tables s2

Supplementary tables

Table S1 Polymorphic SSR markers screened from 563 genomic SSR markers (http://wheat.pw.usda.gov/GG2/index.shtml)

Table S2 Data for Vrn gene primers and SSR primers developed from T .urartu genome sequences

Table S3 Comparison of genetic maps for einkorn wheat, T. aestivum and T. durum

Table S4 Distribution of markers with segregation distortion at seven linkage groups at P = 0.05 and 0.01 Table S5 Detailed information of 19 segregation distortion regions (SDRs) on six chromosomes

Table S6 Proportion of relative segregation distortion ratios of three types of markers at each chromosome

Table S7 Phenotypic performances and distribution parameters (a) and correlations coefficients (b) for four quantitative traits of parents and RILs in six environments

Table S8 Correlation coefficients between HD, SPL, SPLN, PA, and PH in the RIL population in six environments

Table S9 Analysis of variance (ANOVA) results from a simple model in which each of the detected QTL are represented by their peak markers

1 Table S1 Polymorphic SSR markers screened from 563 genomic SSR markers (http://wheat.pw.usda.gov/GG2/index.shtml) (Supplementary Tables.xlsx)

2 Table S2 Data for Vrn gene primers and SSR primers developed from T .urartu genome sequences (Supplementary Tables.xlsx)

3 Table S3 Comparison of genetic maps for einkorn wheat, T. aestivum and T. durum (Supplementary Tables.xlsx)

4 Table S4 Distribution of markers with segregation distortion at seven linkage groups at P = 0.05 and 0.01 SSR in SSR in Total Chr. DArT Protein Gene M(3) RFLP STS(4) Ratio (%) Ta(1) Tu(2) Number 1A 23 (6) 2 (1) 7 (1) 2 (0) 1 (1) 0 (0) 7 (3) 0 (0) 42 (12) 38.18 (10.90) 2A 27 (11) 1 (0) 10 (5) 0 (0) 0 (0) 0 (0) 6 (6) 0 (0) 44 (22) 41.12 (20.56) 3A 21 (8) 2 (0) 18 (2) 0 (0) 0 (0) 0 (0) 3 (0) 17 (9) 61 (19) 32.28 (10.05) 4A 9 (4) 0 (0) 1 (0) 0 (0) 0 (0) 1 (1) 0 (0) 0 (0) 11 (5) 11.00 (5.00) 5A 34 (29) 10 (9) 7 (5) 0 (0) 1 (1) 0 (0) 21 (13) 0 (0) 73 (57) 47.71 (37.25) 6A 1 (0) 0 (0) 0 (0) 0 (0) 0 (0) 0 (0) 1 (0) 0 (0) 2 (0) 1.77 (0.00) 7A 49 (46) 8 (4) 5 (5) 0 (0) 1 (1) 0 (0) 2 (2) 0 (0) 65 (58) 42.21 (37.67) Total 164 (104) 23 (14) 48 (18) 2 (0) 3 (3) 1 (1) 40 (24) 17 (9) 298 (173) 32.18 (18.68) (1) Ta genomic SSR markers and primer sequences in hexaploid wheat were downloaded from GrainGenes (http://wheat.pw.usda.gov/GG2/index.shtml). (2) Tu genomic SSR markers and primer sequences were designed according to T. urartu genome sequences (Ling et al. 2013). (3) Morphological markers, leaf hairiness, vernalization requirement and aleuronic layer color of seed. (4) STS markers were soured from Gawronski and Schnurbusch (2012). (5) At each cell, N1 (N2) represent marker numbers segregation distortion in the level P = 0.05 (N1) and 0.01 (N2).

5 Table S5 Detailed information of 19 segregation distortion regions (SDRs) on six chromosomes SDR Preferred Start End Start marker End marker Marker Subtotal Lengt Subtotal allelea (cM) (cM) No. marker h (cM) length number (cM) SDR-1A.1 ♀ 54.78 55.74 Xrz166 Xrz251 3 0.96 SDR-1A.2 ♀ 62.98 69.27 Xwec47 CASA0374 8 6.29 SDR-1A.3 ♀ 102.44 131.30 XwPt-860875 XwPt-861458 18 28.87 SDR-1A.4 ♀ 166.94 174.27 XwPt-469544 XwPt-1685 9 38 7.34 43.46 SDR-2A.1 ♂ 48.69 103.78 XwPt-470187 CASA0180-1 44 44 55.09 55.09 SDR-3A.1 ♂ 0.00 8.81 XwPt-7486 XwPt-6012 5 8.81 SDR-3A.2 ♂ 18.10 20.65 Xcfd2-3 XwPt-470073 3 2.55 SDR-3A.3 ♀ 68.51 76.72 Xwec53 CASA0194 8 8.21 SDR-3A.4 ♀ 93.35 98.37 Xabc176 AS_PCR_149_150-10.5 4 5.01 SDR-3A.5 ♂ 222.49 226.47 Tu3AL5127.1 Xwec57 6 3.99 SDR-3A.6 ♂ 227.54 229.70 PAV_185_186-93.2 AS_PCR_117_118-92.2 3 2.16 SDR-3A.7 ♂ 235.21 243.88 Tu3AL5205 Tu3AL5071.2 21 50 8.67 39.41 SDR-4A.1 ♂ 36.34 61.95 XwPt-470231 XwPt-9833 8 8 25.61 SDR-5A.1 ♂ 7.61 50.15 XwPt-377038 Xbcd926 53 42.54 SDR-5A.2 ♂ 54.18 60.77 Xwec9-3 Xwec-9-3 3 6.59 SDR-5A.3 ♂ 107.33 117.08 Xbcd1030 Tu3AL5117.1 11 67 9.75 58.89 SDR-7A.1 ♀ 0.00 72.12 Tu3AL5061.1 XwPt-861757 55 72.12 SDR-7A.2 ♀ 77.89 82.41 XwPt-470359 Xbarc174 4 4.52 SDR-7A.3 ♂ 183.89 219.93 Tu3AL5322 XwPt-860857 6 65 36.04 112.68 Total 272 335.14 a ♀, KT-1; ♂, KT3-5.

6 Table S6 Proportion of relative segregation distortion ratios of three types of markers at each chromosome Chr. DArT SSR in Ta (1) SSR in Tu (2) RFLP

1A 31.08% 18.18% 63.64% 70.00% 2A 39.13% 14.29% 62.50% 42.86% 3A 24.42% 14.29% 34.62% 18.75% 4A 13.43% 0.00% 8.33% 0.00% 5A 39.53% 52.63% 63.64% 63.64% 6A 1.16% 0.00% 0.00% 10.00% 7A 42.24% 57.14% 38.46% 22.22% Total 28.08% 30.26% 38.10% 37.74% (1) Ta genomic SSR markers and primer sequences in hexaploid wheat were downloaded from GrainGenes (http://wheat.pw.usda.gov/GG2/index.shtml). (2) Tu genomic SSR markers and primer sequences were designed according to T. urartu genome sequences (Ling et al. 2013).

7 Table S7 Phenotypic performances and distribution parameters (a) and correlations coefficients (b) for four quantitative traits of parents and RILs in six environments (a). Trait Env.(1) KT1-1 KT3-5 RIL Min.(2) RIL Max.(3) RIL Ave.(4) SD(5) H (%)(6) 206.0 HD E1 191.00 184.00 217.00 195.55 8.81 70.27 0 217.0 Heading date (days) E2 202.00 190.00 232.00 204.52 8.15 0 223.0 E3 210.00 203.00 235.00 215.20 6.94 0 219.0 E4 197.00 182.00 228.00 200.61 12.01 0 221.0 E5 198.00 198.00 242.00 208.26 11.32 0 202.0 E6 190.00 180.00 227.00 197.43 12.89 0 SPL E1 11.50 8.70 7.00 16.33 10.02 1.78 93.91 Spike length (cm) E2 15.60 8.08 6.97 17.00 10.53 2.15 E3 13.63 8.63 6.50 15.83 10.52 1.95 E4 14.33 8.25 8.43 16.50 11.66 1.83 E5 14.00 8.50 7.50 24.67 11.36 2.76 E6 NA(7) 8.40 6.80 16.50 10.97 2.18 SPLN E1 28.00 25.80 18.30 42.50 28.89 5.45 93.02 Spikelet number/spike E2 31.00 27.00 17.00 38.00 27.19 5.05 E3 30.50 28.67 17.00 44.00 28.35 5.27 E4 32.33 24.50 18.50 49.00 32.24 5.56 E5 32.00 27.00 18.50 44.00 28.49 5.87 E6 NA 27.00 17.33 47.67 28.99 5.98 PA (scale) E1 1.00 4.00 1.00 4.00 2.85 0.98 83.95 Plant architecture(2) E3 1.00 3.00 1.00 3.00 2.58 0.58 E4 1.00 4.00 1.00 4.00 3.04 1.03 E5 1.00 4.00 1.00 4.00 2.51 1.11 E6 3.00 4.00 2.00 4.00 3.62 0.51 109.5 PH (cm) E1 101.50 93.90 171.88 121.05 15.36 82.35 0 Plant height (cm) E2 NA NA 76.63 141.83 106.08 14.80 120.2 E3 107.33 72.00 148.00 115.46 16.35 5 132.5 E4 105.00 69.00 163.50 124.29 15.77 0 133.0 E5 124.33 83.83 154.00 120.68 12.72 0 E6 NA 125.77 89.83 155.67 127.09 14.06

(b). Trait Env. E1 E2 E3 E4 E5 E6 HD E1 1 Heading date (days) E2 0.8514** 1 E3 0.8796** 0.8037** 1 E4 0.8722** 0.8172** 0.8519** 1 E5 0.7287** 0.6568** 0.755** 0.7861** 1 E6 0.7444** 0.6722** 0.7666** 0.7556** 0.7409** 1 SPL E1 1 Spike length (cm) E2 0.613** 1 E3 0.6985** 0.8219** 1

8 E4 0.6571** 0.7304** 0.7141** 1 E5 0.3931** 0.4876** 0.4553** 0.3774** 1 E6 0.4955** 0.681** 0.6931** 0.7276** 0.4728** 1 SPLN E1 1 Spikelet number/spike E2 0.8205** 1 E3 0.8392** 0.8106** 1 E4 0.7103** 0.7333** 0.7431** 1 E5 0.7842** 0.811** 0.7895** 0.7616** 1 E6 0.7012** 0.6974** 0.7738** 0.7656** 0.8036** 1 PH E1 1 Plant height (cm) E2 0.6456** 1 E3 0.7645** 0.7094** 1 E4 0.5024** 0.4829** 0.6602** 1 E5 0.5478** 0.4787** 0.5506** 0.4785** 1 E6 0.5582** 0.4629** 0.575** 0.5207** 0.5796** 1 (1) Environment: E1, E2, E3, E4, E5 and E6 represent Beijing 2011, Beijing 2012, Beijing 2013, Beijing 2014, Zhengzhou 2013 and Zhengzhou 2014, respectively. (2) Minimum value among RILs. (3) Maximum value among RILs. (4) Average value for RILs. (5) Standard deviation of each set of phenotypic data. (6) Broad sense heritability. (7) NA, data not collected. (8) **, P = 0.01.

9 Table S8 Correlation coefficients between HD, SPL, SPLN, PA, and PH in the RIL population in six environments Env. HD- HD- HD- SPL- SPL- SPLN- SPLN- PA- HD-PA SPL-PA (1) SPL SPLN PH SPLN PH PA PH PH - - - 0.6164* 0.6479* 0.2629 0.3652* 0.6094 0.087 E1 * 0.8725** * ** 0.6878** * ** -0.5538** 0.4675** 3 0.5989* 0.4404 E2 * 0.7606** NA(2) 0.1143 0.8472** NA ** NA 0.3612** NA - - - 0.6440* 0.5070* 0.2554 0.3837* 0.6835 0.065 E3 * 0.7192** * ** 0.8065** * ** -0.3162** 0.5170** 6 - - 0.4439* - - 0.5050 0.3811* 0.122 E4 * 0.7214** 0.5411** 0.1879 0.7582** 0.2441* ** * 0.3278** 4 - 0.4408* - - 0.2731* 0.3535 0.088 E5 * 0.7982** 0.2221* 0.1034 0.5466** * ** -0.1407 0.1841* 7 0.6969* 0.3705 0.6531 0.040 E6 * 0.8011** -0.1210 ** 0.8239** -0.0823 ** -0.0336 0.5782** 1 (1) Environment: E1, E2, E3, E4, E5 and E6 represent Beijing 2011, Beijing 2012, Beijing 2013, Beijing 2014, Zhengzhou 2013 and Zhengzhou 2014, respectively. (2) NA, data not collected. (3) *, P = 0.05; **, P = 0.01.

10 Table S9 Analysis of variance (ANOVA) results from a simple model in which each of the detected QTL are represented by their peak markers Traita Effect P Variation R2 (%) Trait Effect P Variation R2 (%) (%) (%) Days to heading (six Spikelet number per environments) 3A.1 <0.0001 37.07 spike (six environments) 3A.1 <0.0001 44.45 5A.1 <0.0001 1.13 7A.1 <0.0001 10.81 7A.1 <0.0001 6.44 3A.1×7A.1 0.0029 0.51 3A.1×5A.1 0.591(NS) 0.01 G model 55.77 3A.1×7A.1 <0.0001 0.00 G×E model 64.41 5A.1×7A.1 0.268(NS) 0.04 G model 44.70 G × E model 77.08 Spike length (six Plant architecture (four environments) 1A.1 <0.0001 5.06 environments) 2A.1 <0.0001 8.83 3A.1 <0.0001 31.28 3A.1 <0.0001 18.81 4A.1 <0.0001 3.52 7A.1 0.0031 1.62 0.4042(NS 4A.2 0.000158 1.47 2A.1×3A.1 ) 0.12 0.3818(NS 5A.1 <0.0001 2.48 2A.1×7A.1 ) 0.15 1A.1×3A.1 0.2436(NS) 0.14 3A.1×7A.1 0.0082 1.30 1A.1×4A.1 0.1672(NS) 0.19 G model 30.83 1A.1×4A.2 0.0205 0.55 G × E model 40.76 1A.1×5A.1 0.6050(NS) 0.03 Plant height (six 3A.1×4A.1 0.2168(NS) 0.15 environments) 1A.1 0.00042 1.57 3A.1×4A.2 0.1677(NS) 0.19 2A.1 <0.0001 9.63 3A.1×5A.1 0.2025(NS) 0.17 4A.1 <0.0001 7.27 4A.1×4A.2 0.4057(NS) 0.07 1A.1×2A.1 0.0120 0.79 0.3495(NS 4A.1×5A.1 0.2266(NS) 0.15 1A.1×4A.1 ) 0.11 0.2444(NS 4A.2×5A.1 0.0740(NS) 0.32 2A.1×4A.1 ) 0.17 G model 45.78 G model 19.53 G × E model 55.11 G × E model 40.10 a The peak markers used to represent the three QTL for HD in the model are PAV_295_296-102.9 (qHD-3A.1), Vrn1 (qHD-5A.1), and FT1-Vrn3 (qHD-7A.1); XwPt-861678 (qSPL-1A.1), PAV_295_296-102.9 (qSPL-3A.1), XwPt-862216 (qSPL-4A.1), XwPt-861528 (qSPL-4A.2), and XwPt-376180 (qSPL-5A.1) for the five QTL for SPL; PAV_295_296-102.9 (qSPLN-3A.1) and FT1-Vrn3 (qSPLN-7A.1) for the two QTL for SPLN; Tu3AL5175.2 (qPA-2A.1), PAV_295_296-102.9 (qPA-3A.1), and XwPt-469984 (qPA-7A.1) for the three QTL for PA; Xrz251 (qPH-1A.1), CASA0912 (qPH-2A.1), and XwPt-5663 (qPH-4A.1) for the three QTL for PH. For each trait, included in the model are the main effects of the QTLs, the first-order interactions among these QTL, and environments (year × locations, not shown). P values are presented for all main and first-order QTL effects. The overall model R2 values for the five phenotypic datasets are provided, and the percent of total phenotypic variation explained by each effect are also given R2 using Genotype (G model) and Genotype by Environment (G × E model).