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.

Early seedling vigor (ESV) is a major breeding target in rice, especially under direct seeding. To identify quantitative trait locus (QTL) affecting ESV, a recombinant inbred line population derived from a cross between 02428 and YZX, two cultivars differing in vigor during early seedling growth, was used for QTL analysis. Nine traits associated with ESV were examined using a high-density map. Of 16 additive loci identified, three were detected in two generations and thus considered stable. Four epistatic interactions were detected, one of which was repeated in two generations. Further analysis of the pyramiding effect of the three stable QTL showed that the phenotypic value could be effectively improved with an increasing number of QTL. These results were combined with results from our previous QTL analysis of the germination index. The lines G58 and G182 combined all the favourable alleles of all three stable QTL for ESV and three QTL for germination speed. These two lines showed rapid germination and strong ESV. A total of 37 candidate differentially expressed genes were obtained from the regions of the three stable QTL by analysis of the dynamic transcriptomic expression profile during the seedling growth period of the two parents. The QTL are targets for ESV breeding and the candidate genes await functional validation. This study provides a theoretical basis and a genetic resource for the breeding of direct-seeded rice.