Combination of quantitative trait locus (QTL) mapping and transcriptome analysis reveals submerged germination QTLs and candidate genes controlling coleoptile length in rice

Submerged germination ability is a key trait of rice (Oryza sativa L.) in the success of water direct seeding. Therefore, mining submerged germination-related loci and seeking high tolerant rice germplasms are important for developing rice direct seeding breeding strategies. Here, we treated 272 recombinant inbred lines (RILs, F-15) from a cross from Luohui 9 (indica) and RPY geng (japonica) with simulated submergence for 7 days. We successfully bred several superior homozygous RILs with high submergence resistance, namely, R53, R137, R148, R176, and R180, via indica and japonica hybridization strategies. Then, the QTL mapping of coleoptile length trait was performed by R/qtl and IciMapping softwares based on the high-density bin marker genetic map and two QTLs responsible for coleoptile length were detected in chromosomes 1 (qCL-1.1) and 3 (qCL-3.1). The haplotype results of RILs showed that the aggregation of elite alleles of these two QTLs in an individual was beneficial to improving the rice submergence tolerance. According to contrasting genotype of qCL-1.1 and qCL-3.1 with different coleoptile lengths, RIL07 (R07) and R180 were selected to further RNA-seq analysis for analyzing the possible molecular mechanisms of rice under submergence stress. Finally, LOC_Os01g04430, LOC_Os01g04530, and LOC_Os03g22720 for qCL-1.1 and qCL-3.1 were characterized to affect submergence stress by the overlapped analysis of two independent sets of RNA-seq data, qRT-PCR verification, and gene sequence alignments. In this study, the submerged germination-related QTLs/genes and high submergence-tolerant RILs provided new genetic resources for breeding rice varieties suitable for direct seeding via molecular breeding strategies in the immediate future.