Fig. 4

Validate a major LTG QTL, qLTG3a, by an F₂ population and BSA sequencing. "aa" represents the HJX74 allele of qLTG3a, and "AA" represents the S6 allele of qLTG3a. Roles of qLTG3a in LTG during seed germination (a) and seed development (c). Dots and bars represent the means and standard deviations of LTG at each time point. Germination data were calculated based on at least four biological replicates during seed germination and nine biological replicates during seed development. b Representative germination images showing different LTG phenotypes between HJX74 and S6. Pictures were taken on the 5th, 7th, and 10th day after sowing. Bar = 1 cm. d Frequency distribution and genetic effects of qLTG3a in a 356-progeny population derived from the cross of HJX74 and S6. The donor parent of S6 is Katy. LTG was evaluated on the 7th day after sowing. The genotypes of individual plants were determined by the InDel P7 marker. The additive effects (a), dominance effects (d), and proportion of the variance explained by the QTL (R²) were estimated based on Model 1. A positive a or d value indicates that the "A" allele increased LTG. * for P < 0.0001 and ns for P ≥ 0.05. e Manhattan plot shows the distribution of SNP-index and ΔSNP-index on 12 chromosomes. The reference genome for BSA sequencing is the indica variety R498 (Shuhui498). The blue and red lines represent 95 and 99% confidence intervals, respectively. The black line shows the ΔSNP-index value of fitting results