RNAseq and data analysis
For RNAseq analysis, RNA was extracted from three replicates of 25 mature seeds of wild type, Mthsfa9-1 and Mthsfa9-2 alleles that were grown together. RNAseq was outsourced to BGI Genomics (Shenzhen, China). RNA quality was checked with an Agilent 2100 Bio analyzer (Agilent RNA 6000 Nano Kit). RNA was sequenced using the DNBseq platform, generating an average 24M reads per sample. The sequencing reads which containing low-quality, adaptor-polluted and high content of unknown base (N) reads were removed and mapping of the clean reads was performed against the Mt4.0 genome. Total mapping ratio was 90%, and unique mapping ratio 78%. DEGs (differential expressed genes) between samples were determined using DEseq2 algorithms. Genes were considered differential when the adjusted P-value was <0.05 and log2FoldChange of 1. On the DEGs, GO (http://www.geneontology.org/) and KEGG (https://www.kegg.jp/) enrichment analysis of annotated different expression gene was performed by Phyper (https://en.wikipedia.org/wiki/Hypergeometric_distribution) based on Hypergeometric test. The significant levels of terms and pathways were corrected by Q value with a rigorous threshold (Q value ≤ 0.05) by Bonferroni. RNAseq data were deposited in the NCBI Gene Expression Omnibus database (accession number GSE98199 and GSExxxx).