Evolution of DNA methylation during the domestication of foxtail millet. Setaria italica

This study aims to study the evolution of DNA methylation in wild and cultivated foxtail millet. The experiment was conducted during the 2020 growing season (June to October) at the experimental station of the Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China (116.34 E, 39.97 N). Plants were grown in a climate chamber under controlled conditions: 28 degree, 70 percent relative humidity, and a light intensity of 165. Genomic DNA was extracted from young leaf tissues (14-day-old) of 20 wild, 20 landrace, and 20 cultivated accessions using the cetyltrimethylammonium bromide (CTAB) method, followed by bisulfite conversion. Sequencing libraries were prepared with the EpiArt DNA Methylation Library Kit for Illumina V3 (NE103) and sequenced on an Illumina NextSeq 500 platform. Total mRNA was isolated from young leaf tissues of 16 wild and 17 landrace accessions using TRIzol reagent (Thermo Fisher Scientific). RNA-seq libraries were prepared for paired-end sequencing on an MGISEQ-2000 platform, producing 150-bp paired-end reads. Small RNA was extracted from total RNA of young leaf tissues of 9 wild and 9 landrace accessions using a NEBNext Small RNA Library Prep Set for Illumina. Sequencing of small RNA libraries was completed on an Illumina NovaSeq 6000 machine.