Small RNA and degradome deep sequencing reveal regulatory roles of miRNAs in response to Sugarcane mosaic virus infection on two contrasting sugarcane lines

Sugarcane (Saccharum officinarium L.), resistant genotype Fuguo 1 (FG1), is registered in the Ministry of Agriculture and Rural Affairs of China Trial Registry (registration number: GPD Sugarcane (2022) 450016), sustaining high resistance against SCMV infection, and obtained by somatic mutation of susceptible cultivar Badila (Nanning, Guangxi, China). Stable growth conditions were supplied at 24-28 temperature with 16:8h of light/dark photoperiod. The first leaf, one-month-old (4-leaf stage) and grown above the ligule, was mechanically infected with sap (at 6 pm). Sap was prepared using crude extract of SCMV-infected leaves with phosphate buffer (PB), stained using 80 mesh quartz. Inoculation was performed using fingers which lightly reciprocate friction five times. Leaves were wrapped with fresh film to maintain humidity. Sampling was performed at different time points after infection. First, sampling was performed without infection (0h). And second, third, fourth, and fifth sampling was performed after 6h, 18h, 48h, and 192h of infection. Each leaf was cut 15 cm, which distributed three inoculation sites, with each about 1 cm wide. A total of 30 samples from five infection sites were collected, each from Badila and FG1. Two replicates from each sample were collected for further analysis. We performed small RNA sequencing on 30 samples from 10 treatments (with 3 replicates per treatment), and mixed the 3 replicates from each treatment for degradation group sequencing.