*2.4. Field Evaluation of the "YNU31-2-4" for Main Agronomic Traits*

We evaluated "YNU31-2-4" in the field to compare its major agronomic traits with those of the parents. We found a significant difference in days-to-heading between "YNU31-2-4" and WT: some plants headed significantly earlier than WT (Table 3; Figure S2B). Heading date was associated negatively with the *Os09g0356200* genotype and positively with the *hst1* genotype. These results support the accuracy of gene-based GWAS [53], and also suggest the potential early flowering function of *hst1* or the effect of unknown flowering-related genes. Grain width, grain thickness, and 1000-grain weight were significantly higher in "YNU31-2-4" plants than WT (Table 3). The *hst1* mutant also had a wider grain than WT [32]. Together these results, at least partly, suggest that *hst1* might be involved in the increase of grain width. In contrast, other important morphological traits of "YNU31-2-4" were highly similar to those of WT, particularly flag leaf color, length, and width, plant height, tiller number

per plant, panicle number per plant, panicle length, spikelet number per panicle, grain yield per plant, aboveground biomass per plant, and grain length (Table 3; Figure S3A–C). (colour). Black, "Yukinko-mai"-type homozygous; red, "Kaijin"-type homozygous; blue, heterozygous. Green bars represent chromosome length.

*Int. J. Mol. Sci.* **2019**, *20*, x FOR PEER REVIEW 6 of 22

**Figure 3.** Sequence Ontology analysis of BC3F2 SNPs/indels. Sequence Ontology is based on SnpEff terms with minor modifications. Closed bars, SNPs; open bars, indels. Black, "Yukinko-mai"-type homozygous, red, "Kaijin"-type homozygous; blue, heterozygous. **Figure 3.** Sequence Ontology analysis of BC3F<sup>2</sup> SNPs/indels. Sequence Ontology is based on SnpEff terms with minor modifications. Closed bars, SNPs; open bars, indels. Black, "Yukinko-mai"-type homozygous, red, "Kaijin"-type homozygous; blue, heterozygous.




