Extreme weather events have increased the number of severe flooding events that affect agriculture, including rice production both in the US and internationally. Heavy rainfall can cause young rice plants to be temporarily completely submerged, a stress that can reduce grain yield or completely destroy the plants. Recently, a new submergence tolerance QTL, qSub8.1 was identified from a population derived from Ciherang-Sub1 and IR10F365 that may have a complementary effect with the known submergence tolerance regulator SUB1A during vegetative stage development. Our ultimate goal is to identify the gene(s) underlying qSub8.1 and investigate its mode of action in enhancing submergence tolerance in conjunction with SUB1A. Toward this goal, three rice varieties, Ciherang-Sub1, Ciherang, and IR64-Sub1, were sequenced with 150 bp pair-end whole genome shotgun sequencing (Illumina HiSeq4000). The Trimmomatic-SOAPdenovo2-MUMmer3 pipeline for genome assembly resulted in approximate genome sizes of 354.4 Mb, 343.7 Mb, and 344.7 Mb, with N50 values of 25.1 kb, 25.4 kb, and 26.1 kb, respectively. A total of 636,243 SNPs were identified, with 83,555 SNPs located on chromosome 8. The genome profile showed that qSub8 region is mainly from Ciherang with a few introgressed segments from IR64-Sub1 and unknown sources. These findings will be used to further characterize qSub8.1 along with transcriptomic data which has recently been generated. To evaluate interactions between qSub8.1 and SUB1A we performed RNA-sequencing transcriptome analyses on the shoot basal region of four genotypes that differ in the presence and absence of both loci/QTL. The data indicate qSub8.1 reinforces the quiescence strategy conferred by SUB1A during submergence. In addition to producing qSub8.1 NILs through the crossing, we are also using CRISPR/Cas9 to knock out the SUB1A allele in Ciherang-Sub1 and the downstream analysis is currently underway. Funded by NIFA 2017-67013-26194.

Keywords: Submergence, rice, SUB1, qSub8.1, genome assembly, genome editing, transcriptomics