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Additional file 7: Figure S5. The morphological characteristics of the stems of d2014 and WT.

Table S8. QTL × environment interactions for yield-related traits detected in the RILs under four environments and the IF2 population under three environments. a RIL, recombinant inbred lines; IF2, the immortalized F2. b AE indicates the additive by designed environment interaction effect. E1, E2, E3, and E4, represent 2014JH, 2015JH, 2016CZ, and 2016JH, respectively. c h2(AE, %) is the contribution rate of additive by environment interaction effect. d DE indicates the dominance by designed environment interaction effect. E1, E2, E3, and E4, represent 2014JH, 2015JH, 2016CZ, and 2016JH, respectively. e h2(DE, %) is the contribution rate of dominance by environment interaction effect. *, **, *** indicate significance at p

Table S5. Pearson’s correlation coefficients between phenotypic performance per se in IF2 population and mid-parent heterosis for those traits. *** Significant at p

Table S3. Pearson’s correlation coefficients among yield-related traits in the RILsa across four environments, the IF2c populations across three environments, and the mid-parent heterosis (MPH) dataset. * Significant at the 0.05 probability level. ** Significant at the 0.01 probability level. The absolute values of Pearson’s correlation coefficients (r2) with bold are equal to or larger than 0.5. EWPE, ear weight per ear; CWPE, cob weight per ear; ED, ear diameter; CD, cob diameter; EL, ear length; RN, row number; KNPR, kernel number per row; KWPE, kernel weight per row; RKP, rate of kernel production. a Pearson’s correlation coefficients (r2) in the first row for each trait are for the RILs. b Pearson’s correlation coefficients (r2) in the second row for each trait are for the IF2 population. c Pearson’s correlation coefficients (r2) in the third row for each trait are for mid-parent heterosis. (DOCX 1433 kb)

Figure S2. Phenotypic variance explained (PVE) by QTL and epistasis interaction (EPI, digenic interaction) effects for nine yield-related traits in the RILs, IF2 population and the MPH dataset. The total PVE for QTL and epistasis was estimated on ICIM-ADD and ICIM-EPI, respectively. ICIM, inclusive composite interval mapping. RIL, recombinant inbred line. IF2, immortalized F2. MPH, mid-parent heterosis. EWPE, ear weight per ear; CWPE, cob weight per ear; EL, ear length; ED, ear diameter; CD, cob diameter; RN, row number; KNPR, kernel number per ear; KWPE, kernel weight per ear; RKP, rate of kernel production. (PPTX 37 kb)

Table S1. List of abbreviations and definitions for the yield-related traits recorded at harvest in a sample of ten ears per plot. (DOCX 16 kb)

Figure S2. Phenotypic variance explained (PVE) by QTL and epistasis interaction (EPI, digenic interaction) effects for nine yield-related traits in the RILs, IF2 population and the MPH dataset. The total PVE for QTL and epistasis was estimated on ICIM-ADD and ICIM-EPI, respectively. ICIM, inclusive composite interval mapping. RIL, recombinant inbred line. IF2, immortalized F2. MPH, mid-parent heterosis. EWPE, ear weight per ear; CWPE, cob weight per ear; EL, ear length; ED, ear diameter; CD, cob diameter; RN, row number; KNPR, kernel number per ear; KWPE, kernel weight per ear; RKP, rate of kernel production. (PPTX 37 kb)

Table S5. Pearson’s correlation coefficients between phenotypic performance per se in IF2 population and mid-parent heterosis for those traits. *** Significant at p

Table S2. The performance of yield-related traits in the RILs, the IF2 population, and the MPH dataset across all environments. EWPE, ear weight per ear; CWPE, cob weight per ear; ED, ear diameter; CD, cob diameter; EL, ear length; RN, row number; KNPR, kernel number per row; KWPE, kernel weight per row; RKP, rate of kernel production. a F1, The cross of 08–641 × YE478. RIL, the recombinant inbred lines. b IF2 and MPH indicate the immortalized F2 population and mid-parent heterosis, respectively. c Mean ± SE represents mean across all environments ± standard error. d MPH (%) = (F1-(P1 + P2)/2)/((P1 + P2)/2)*100%. (DOCX 18 kb)

Additional file 3: Figure S1. The br2 allelism test for d2014.

Additional file 4: Figure S2. Comparison of certain internode length between d2014 and WT at the 12-leaf, 14-leaf, and 20-leaf stages.

Table S3. Pearson’s correlation coefficients among yield-related traits in the RILsa across four environments, the IF2c populations across three environments, and the mid-parent heterosis (MPH) dataset. * Significant at the 0.05 probability level. ** Significant at the 0.01 probability level. The absolute values of Pearson’s correlation coefficients (r2) with bold are equal to or larger than 0.5. EWPE, ear weight per ear; CWPE, cob weight per ear; ED, ear diameter; CD, cob diameter; EL, ear length; RN, row number; KNPR, kernel number per row; KWPE, kernel weight per row; RKP, rate of kernel production. a Pearson’s correlation coefficients (r2) in the first row for each trait are for the RILs. b Pearson’s correlation coefficients (r2) in the second row for each trait are for the IF2 population. c Pearson’s correlation coefficients (r2) in the third row for each trait are for mid-parent heterosis. (DOCX 1433 kb)

Additional file 2: Table S2. Plant height separation performance in F2 and BC1 populations.

Additional file 6: Figure S4. The analysis of protein domains of PGP1-T01 and PGP1-T02.

Table S2. The performance of yield-related traits in the RILs, the IF2 population, and the MPH dataset across all environments. EWPE, ear weight per ear; CWPE, cob weight per ear; ED, ear diameter; CD, cob diameter; EL, ear length; RN, row number; KNPR, kernel number per row; KWPE, kernel weight per row; RKP, rate of kernel production. a F1, The cross of 08–641 × YE478. RIL, the recombinant inbred lines. b IF2 and MPH indicate the immortalized F2 population and mid-parent heterosis, respectively. c Mean ± SE represents mean across all environments ± standard error. d MPH (%) = (F1-(P1 + P2)/2)/((P1 + P2)/2)*100%. (DOCX 18 kb)

Table S6. Pearson’s correlation coefficients between phenotypic variation and genome marker heterozygosity. a Correlation between performance per se in IF2 population and percentage of heterozygous loci. b Correlation between mid-parent heterosis and the percentage of heterozygous loci. ***, significant at p

Table S1. List of abbreviations and definitions for the yield-related traits recorded at harvest in a sample of ten ears per plot. (DOCX 16 kb)

Table S7. Epistatic interactions for yield-related traits and mid-parent heterosis detected in the RILs and IF2 population across all environments. a EWPE, ear weight per ear; CWPE, cob weight per ear; CD, cob diameter; EL, ear length; RN, row number; KNPR, kernel number per row; KWPE, kernel weight per row; RKP, rate of kernel production. b Interval of the first QTL i. c Chromosome ID at the first scanning position. d A_i Additive effect of the QTL i. e D_i Dominance effect of the QTL i. f Interval of the second QTL j. g Chromosome ID at the second scanning position. h A_j Additive effect of the QTL j. i D_j Dominance effect of the QTL j. j AA: Estimated additive by the additive effect of QTLs at the two scanning positions. k AD: Estimated additive by dominance effect of QTLs at the two scanning positions. m DA: Estimated dominance by the additive effect of QTLs at the two scanning positions. n DD: Estimated dominance by dominance effect of QTLs at the two scanning positions. l h2(%): Heritability for epistatic QTL effects. The interval in bold was co-located in QTLs associated with the same trait via combined analysis across all environments. *, **, *** indicate significance at p

Table S7. Epistatic interactions for yield-related traits and mid-parent heterosis detected in the RILs and IF2 population across all environments. a EWPE, ear weight per ear; CWPE, cob weight per ear; CD, cob diameter; EL, ear length; RN, row number; KNPR, kernel number per row; KWPE, kernel weight per row; RKP, rate of kernel production. b Interval of the first QTL i. c Chromosome ID at the first scanning position. d A_i Additive effect of the QTL i. e D_i Dominance effect of the QTL i. f Interval of the second QTL j. g Chromosome ID at the second scanning position. h A_j Additive effect of the QTL j. i D_j Dominance effect of the QTL j. j AA: Estimated additive by the additive effect of QTLs at the two scanning positions. k AD: Estimated additive by dominance effect of QTLs at the two scanning positions. m DA: Estimated dominance by the additive effect of QTLs at the two scanning positions. n DD: Estimated dominance by dominance effect of QTLs at the two scanning positions. l h2(%): Heritability for epistatic QTL effects. The interval in bold was co-located in QTLs associated with the same trait via combined analysis across all environments. *, **, *** indicate significance at p

Table S4. Main feature of QTLs for yield-related traits and for mid-parental heterosis for those traits from the RILs and IF2 population via single environment analysis. a The nomination of QTL is made as follows: a “q” standing for the abbreviation of QTL, the abbreviation of the trait, an “S” standing for single environment analyses, a number standing for chromosome, and another for physical order. EWPE, ear weight per ear; CWPE, cob weight per ear; ED, ear diameter; CD, cob diameter; EL, ear length; RN, row number; KNPR, kernel number per row; KWPE, kernel weight per row; RKP, rate of kernel production. b RIL, recombinant inbred lines; IF2, the immortalized F2; MPH, mid-parental heterosis derived from the RIL and IF2 populations. c Env, environment; E1, 2014Jinghong; E2, 2015Jinghong; E3, 2016Chongzhou; E4, 2016Jinghong. d Chr, chromosome. e A, additive effect; Negative additive values indicate that the allele for increasing trait value is contributed by the parent 08–641; Positive additive values indicate that the allele for increasing trait value is contributed by another parent Ye478. f D, dominance effect. g PVE, phenotypic variance explained by QTL. (DOCX 70 kb)

Table S6. Pearson’s correlation coefficients between phenotypic variation and genome marker heterozygosity. a Correlation between performance per se in IF2 population and percentage of heterozygous loci. b Correlation between mid-parent heterosis and the percentage of heterozygous loci. ***, significant at p

Additional file 5: Figure S3. Different mutation sites of br2 alleles.

Supplemental Material. This file contains Tables S1â S3 and all the Figures S1â S7. (PDF 1647 kb)