Insights into the Regulation of Rice Seed Storability by Seed Tissue-Specific Transcriptomic and Metabolic Profiling

Abstract

Non-dormant seeds are continuously aging and deteriorating during storage, leading to declining seed vigor, which is a challenge for the rice seed industry. Improving the storability of seeds is of great significance to ensure the quality of rice and national food security. Through a set of chromosome segment substitution lines population constructed using japonica rice NIP as donor parent and indica rice ZS97 as recurrent parent, we performed seed storability QTL analysis and selected four non-storable NILs to further investigate the storability regulatory mechanisms underlying it. The seeds were divided into four tissues, which were the embryo, endosperm, aleurone layer, and hull, and tissue-specific transcriptome and metabolome analyses were performed on them. By exploring the common differentially expressed genes and differentially accumulated metabolites, as well as the KEGG pathway of the four non-storable NILs, we revealed that the phenylpropanoid biosynthesis pathway and diterpenoid biosynthesis pathway played a central role in regulating seed storability. Integrated analysis pinpointed 12 candidate genes that may take part in seed storability. The comprehensive analysis disclosed the divergent and synergistic effect of different seed tissues in the regulation of rice storability.

Transcriptomic Profiling of Two Rice Thermo-Sensitive Genic Male Sterile Lines with Contrasting Seed Storability after Artificial Accelerated Aging Treatment

“…The number of DEGs was higher in S1146S than in SD26S (Figure 2C), which might suggest that the storage-tolerant line S1146S underwent a more complex response than the storage-susceptible SD26S during aging stress. This finding differs from previous studies [47]. Identifying the key mechanisms of seed aging response in the storage-tolerant line S1146S will help us to introduce its storability into the breeding of superior hybrid rice.…”

Genome-Wide Association Study Reveals the Genetic Basis of Seed Germination in Japonica Rice

“…In addition, these stable loci were close to the QTLs reported in previous studies using association and biparental mapping populations. For example, qGR1.1 was found near microsatellite marker RM8095 associated with shoot length [41]; qGR2.1 coincided with the region of qSST2.3 for seed storability [42]; qGR3.1 and qGR7.1 were found to overlap with the intervals of qSD3 BR and qDOM7.1 for seed dormancy, respectively [43,44]; qGR8.1 co-localized with the regions of qSURE8.1 for seed reserve utilization efficiency and qSG8.2 for seed germination [13,45]; qGR9 overlapped with the intervals of qDOR-9-1 for seed dormancy and qSSn-9 for seed storability [46,47]. The above observations overlap with previous findings not only validate the power of a GWAS for identifying significant loci associated with seed germination, but also suggest that the six stable loci detected in this study can be developed as functional molecular markers for rice breeding.…”

Genome-Wide Tissue-Specific Genes Identification for Novel Tissue-Specific Promoters Discovery in Soybean

“…Photosynthetic starch/sucrose formation occurring in leaves was related to photosynthetic and nitrogen source [ 58 ]. The gmx00904 (diterpenoid biosynthesis) pathway was enriched in two seed-specific genes, which were involved in regulating rice seed storability [ 59 ]. When focusing on the root, a specific pathway, gmx00590 (arachidonic acid metabolism) was significantly enriched.…”