The stigma exsertion rate (SER) is a complex agronomy phenotype controlled by multiple genes and climate and a key trait affecting the efficiency of hybrid rice seed production. Using a japonica two-line male sterile line (DaS) with a high SER as the donor and a tropical japonica rice (D50) with a low SER as the acceptor to construct a near-isogenic line [NIL (qSE4DaS)]. Populations were segregated into 2,143 individuals of BC3F2 and BC4F2, and the stigma exsertion quantitative trait locus (QTL) qSE4 was determined to be located within 410.4 Kb between markers RM17157 and RM17227 on chromosome 4. Bioinformatic analysis revealed 13 candidate genes in this region. Sequencing and haplotype analysis indicated that the promoter region of LOC_Os04g43910 (ARF10) had a one-base substitution between the two parents. Further Reverse Transcription-Polymerase Chain Reaction (RT-PCR) analysis showed that the expression level of ARF10 in DaS was significantly higher than in D50. After knocking out ARF10 in the DaS background, it was found that the SER of arf10 (the total SER of the arf10-1 and the arf10-2 were 62.54 and 66.68%, respectively) was significantly lower than that of the wild type (the total SER was 80.97%). Transcriptome and hormone assay analysis showed that arf10 had significantly higher auxin synthesis genes and contents than the wild type and the expression of auxin signaling-related genes was significantly different, Similar results were observed for abscisic acid and jasmonic acid. These results indicate that LOC_Os04g43910 is mostly likely the target gene of qSE4, and the study of its gene function is of great significance for understanding the molecular mechanisms of SER and improving the efficiency of hybrid seed production.

Dormancy is a complex agronomy phenotype controlled by multiple signaling and a key trait repressing pre-harvest sprouting (PHS). However, the signaling network of dormancy remains unclear. In this study, we used Zhonghua11 (ZH11) with a weak dormancy, and Introgression line (IL) with a strong dormancy to study the mechanism of hormones and reactive oxygen species (ROS) crosstalk regulating rice dormancy. The germination experiment showed that the germination rate of ZH11 was 76.86%, while that of IL was only 1.25%. Transcriptome analysis showed that there were 1658 differentially expressed genes (DEGs) between IL and ZH11, of which 577 were up-regulated and 1081 were down-regulated. Additionally, DEGs were mainly enriched in oxidoreductase activity, cell periphery, and plant hormone signal transduction pathways. Tandem mass tags (TMT) quantitative proteomics analysis showed 275 differentially expressed proteins (DEPs) between IL and ZH11, of which 176 proteins were up-regulated, 99 were down-regulated, and the DEPs were mainly enriched in the metabolic process and oxidation-reduction process. The comprehensive transcriptome and proteome analysis showed that their correlation was very low, and only 56 genes were co-expressed. Hormone content detection showed that IL had significantly lower abscisic acid (ABA) contents than the ZH11 while having significantly higher jasmonic acid (JA) contents than the ZH11. ROS content measurement showed that the hydrogen peroxide (H2O2) content of IL was significantly lower than the ZH11, while the production rate of superoxide anion (O2.−) was significantly higher than the ZH11. These results indicate that hormones and ROS crosstalk to regulate rice dormancy. In particular, this study has deepened our mechanism of ROS and JA crosstalk regulating rice dormancy and is conducive to our precise inhibition of PHS.

Preharvest sprouting (PHS), a deleterious phenotype that occurs frequently in rice growing regions with high temperature and precipitation, negatively affects yield, quality, and processing. Seed dormancy can prevent PHS. We report discovery of qSDR3.1, a new quantitative trait locus (QTL) for seed dormancy in rice. knockout lines of qSDR3.1 exhibited significant reduction in PHS. The qSDR3.1 locus negatively regulated seed dormancy by directly inhibiting the transcriptional activity of ABSCISIC ACID INSENSITIVE5 (ABI5). Haplotype analysis showed that qSDR3.1 was divided into five haplotypes and three amino acid (aa) types. The 102nd (aa102) and 105th (aa105) amino acids of qSDR3.1 were the key amino acids responsible for the differences in dormancy between Xian and Geng. Genetic diversity analysis revealed that qSDR3.1 was artificially selected during domestication. We proposed a two-line model for the process of rice dormancy domestication from wild rice to Xian and Geng, and we provide new candidate genes and germplasm for genetic improvement of rice seed dormancy.

Rice is a major food crop across the globe, but the frequent occurrence of rice blast in recent years has seriously affected the yield of rice. In addition, fragrance rice is becoming increasingly popular among consumers. In this study, the fragrant rice variety Wenxiang-1 was used as the donor of the fragrance gene badh2, and the rice variety R1179 was used as the donor of rice blast resistance gene Pi2. Plants that were homozygous for both Pi2 and badh2 were selected using marker-assisted selection (MAS) applied to the Wenxiang-1/R1179 F2 segregation population with the functional markers Pi2-1 and Badh2-1 as well as whole-genome-SNP-genotyping technology. Finally, “elite” rice varieties R365 and R403 that had both high levels of rice blast resistance (level 3 and 4) and fragrance (0.650 and 0.511 mg/kg) were bred. Genetic composition analysis indicated that 40.67% of the whole genome of R365 was inherited from Wenxiang-1, while 59.33% was inherited from R1179. Similarly, 46.26% of the whole genome of R403 was inherited from Wenxiang-1, while 53.74% was inherited from R1179. These new hybrid lines with R365 and R403 as the male parents also exhibit high yield per hectare, especially C815S/R365 and Yu03S/R403 F1, with yields per hectare of 9.93 ± 0.15 and 9.6 ± 0.17 tons. These plants also possess high levels of rice blast resistance (level 3 and 4) and fragrance (0.563 and 0.618 mg/kg).

The use of male sterile lines (MSLs) of rice is essential for heterosis utilization. However, MSLs have a common defect in the elongation of the uppermost internode, eventually leading to incomplete panicle exsertion, blocking pollination, and reducing the hybrid rice seed yield. Previously, the elongated uppermost internode 1 (EUI1) was identified as an active gibberellin-deactivating enzyme that plays a key role in panicle exsertion from the flag leaf sheath in rice (Oryza sativa L.). We used an adenine base editor to edit EUI1 and obtained two types of homozygous transgenic plants (eui1-1 and eui1-2). The transcription and translation levels of EUI1 in the two mutants were significantly lower than in the wild type, as was the oxidation activity of EUI1 to active gibberellins (GAs), which also decreased. The contents of the plant hormones GA1, GA3, and GA4 in eui1-1 (1.64, 1.55, and 0.92 ng/g) and eui1-2 (0.85, 0.64, and 0.65 ng/g) panicles were significantly higher than the wild type (0.70, 0.57, and 0.42 ng/g). The uppermost internode lengths of the mutant were 26.5 and 23.6 cm, which were significantly longer than that of the wild type (18.0 cm), and the cell lengths of the mutant were 161.10 and 157.19 μm, which were longer than that of the wild type (89.28 μm). Our results indicate that the adenine base editing system could increase the content of endogenous bioactive GAs in young panicles by fine-tuning EUI1 activity, reduce the defect of panicle enclosure in MSLs and increase the yield of hybrid rice seed production.