Direct seeding of rice (DS) has been widely adopted due to reduced labor cost and simpler cultivation practices. However, anaerobic flooding conditions reduce seed germination and seedling establishment. Here, a genome-wide association study (GWAS) of four coleoptile traits using 572 rice accessions subjected to 3 d of anaerobic conditions was conducted. The traits were coleoptile length (CL), coleoptile surface area (CSA), coleoptile volume (CV), and coleoptile diameter (CD). Ninety two QTL were identified, with 59 overlapping with previously reported loci. Two rice varieties (C126 and C261) with contrasting coleoptile lengths were selected for multi-omics analyses. A specific anaerobic-responsive blue module was identified by weighted gene co-expression network analysis (WGCNA). Thirty six candidate genes were screened, including OsMYB48 that was predominantly localized in the nucleus. Loss-of-function OsMYB48 mutants exhibited significantly increased coleoptile length relative to the control under 4 d of anaerobic conditions. Endogenous hormone measurements revealed that the content of 1-aminocyclopropanecarboxylic acid (ACC), the ethylene precursor, was significantly increased in the ko-osmyb48-1 mutants. Ethylene-related genes OsACS1 and OsACO2 were also upregulated in the mutants. OsMYB48 DAP-seq identified 31 potential target genes, including WB1 and OsBURP16. Hence, anaerobic-responsive gene OsMYB48 likely acts as a transcriptional repressor of coleoptile elongation under anaerobic germination conditions, probably via the ethylene signaling pathway. This work provides a theoretical basis and genetic resources for breeding rice lines with high germination when directly sown.

Bacterial leaf streak (BLS), caused by Xanthomonas oryzae pv. oryzicola (Xoc), is a bacterial disease affecting rice production in Asia and Africa, whose severity is expected to increase with climate change. Identification of new quantitative-trait loci (QTL) or resistance genes for BLS resistance is essential for developing resistant rice. A genome-wide association study to identify QTL associated with BLS resistance was conducted using phenotypic and genotypic data from 429 rice accessions. Of 47 QTL identified, 45 were novel and two co-localized with previously reported QTL or genes conferring BLS resistance. qBLS6.2 on chromosome 6 explained the greatest phenotypic variation. Combined analysis of differential expression and annotations of predicted genes near qBLS6.2 based on haplotype and disease phenotype identified OsBLS6.2 (LOC_Os06g02960) as a candidate gene for qBLS6.2. OsBLS6.2 knockout plants showed higher resistance to Xoc than wild-type plants. Many other candidate genes for resistance to Xoc were identified.