In molecular breeding of super rice, it is essential to isolate the best quantitative trait loci (QTLs) and genes of leaf shape and explore yield potential using large germplasm collections and genetic populations. In this study, a recombinant inbred line (RIL) population was used, which was derived from a cross between the following parental lines: hybrid rice Chunyou84, that is, japonica maintainer line Chunjiang16B (CJ16); and indica restorer line Chunhui 84 (C84) with remarkable leaf morphological differences. QTLs mapping of leaf shape traits was analyzed at the heading stage under different environmental conditions in Hainan (HN) and Hangzhou (HZ). A major QTL qLL9 for leaf length was detected and its function was studied using a population derived from a single residual heterozygote (RH), which was identified in the original population. qLL9 was delimitated to a 16.17 kb region flanked by molecular markers C-1640 and C-1642, which contained three open reading frames (ORFs). We found that the candidate gene for qLL9 is allelic to DEP1 using quantitative real-time polymerase chain reaction (qRT-PCR), sequence comparison, and the clustered regularly interspaced short palindromic repeat-associated Cas9 nuclease (CRISPR/Cas9) genome editing techniques. To identify the effect of qLL9 on yield, leaf shape and grain traits were measured in near isogenic lines (NILs) NIL-qLL9^CJ16 and NIL-qLL9^C84, as well as a chromosome segment substitution line (CSSL) CSSL-qLL9^KASA with a Kasalath introgressed segment covering qLL9 in the Wuyunjing (WYJ) 7 backgrounds. Our results showed that the flag leaf lengths of NIL-qLL9^C84 and CSSL-qLL9^KASA were significantly different from those of NIL-qLL9^CJ16 and WYJ 7, respectively. Compared with NIL-qLL9^CJ16, the spike length, grain size, and thousand-grain weight of NIL-qLL9^C84 were significantly higher, resulting in a significant increase in yield of 15.08%. Exploring and pyramiding beneficial genes resembling qLL9^C84 for super rice breeding could increase both the source (e.g., leaf length and leaf area) and the sink (e.g., yield traits). This study provides a foundation for future investigation of the molecular mechanisms underlying the source–sink balance and high-yield potential of rice, benefiting high-yield molecular design breeding for global food security.

Root growth and development is an important indicator of root-zone hypoxia tolerance in rice. Melatonin has been suggested to function as a crucial regulator in modulating root growth and improving plant abiotic stress resistance. To explore the role and potential mechanism of melatonin in regulating the root growth under root-zone hypoxia stress, rice seedlings were treated with hypoxia (oxygen level at 0.9–2.1 mg·L⁻¹), combined with or without a 20 μmol·L⁻¹ melatonin pretreatment under a hydroponic condition. The results showed that the exogenous application of melatonin significantly alleviated the inhibition of the rice root growth that was induced by the hypoxia stress. The morphological–phenotypic analyses showed that after the melatonin pretreatment, the primary root length, lateral root length, and lateral root density increased by 11.6%, 8.2%, and 36.8%, respectively, under hypoxia stress. The physiological–biochemical analyses showed that the exogenous melatonin significantly increased the root activity and O₂ influx in the root meristem zone under hypoxia stress to 1.5 times that observed in the hypoxia stress group. The melatonin pretreatment significantly improved the activity of superoxide dismutase (SOD) and decreased the accumulation of superoxide anions (O₂^•−) in the seedling roots, whereas it increased the content of hydrogen peroxide (H₂O₂) under hypoxia stress. The exogenous melatonin pretreatment significantly increased the content of indole-3-acetic acid (IAA) by 51.5% in the rice roots compared to the plants without melatonin pretreatment under hypoxia stress. Quantitative real-time PCR (qRT-PCR) analyses revealed that the melatonin pretreatment induced the expression of OsPIN1a~1d, OsPIN8, OsPIN9, OsAUX1, OsARF19, and OsGH3-2 in the rice seedling roots under aerated conditions, whereas it only obviously upregulated the expression of OsPIN1b, OsPIN2, and OsGH3-2 under hypoxia stress. These results indicate that melatonin positively regulates root growth and development under hypoxia stress, through improving the antioxidant system and directly or indirectly activating the auxin signaling pathway. This study demonstrates the important role of melatonin to modulate root growth under hypoxia stress, providing a new strategy for improving hypoxia tolerance.

Water deficit is a significant abiotic stress affecting crop growth and production. While many studies have indicated that salicylic acid (SA) plays a crucial role in mitigating the detrimental effects of environmental stress on plants, its mechanism regulating the photosynthetic adaptability of maize seedlings under water deficit is still unclear. This study aimed to investigate the impact of exogenous SA on maize seedling performance under polyethylene glycol (PEG)-induced water deficit. The results showed that PEG treatment destroyed the integrity of chloroplast and reduced chlorophyll content and photosynthesis rate (Pn), leading to growth retardation of maize seedlings with lower biomass accumulation and leaf relative water content (RWC). Moreover, chlorophyll fluorescence index, including potential photochemical activity (Fv/Fo), maximum Photosystem II (PSII) quantum yield (Fv/Fm), and energy captured by PSII reaction center for electron transfer (Eto/RC), were decreased, but energy dissipated by unit reaction center (DIo/RC) was enhanced in maize seedlings under water deficit. In addition, PEG treatment also significantly declined the activity of Rubisco and Rubisco activase (RCA) in maize seedlings. In contrast, SA treatment enhanced the content of chlorophyll, as well as the transcription level of psbA, and RCA and Rubisco small subunit (rbcS) reduced the damaging effects of PEG treatment by protecting the integrity of chloroplast and repairing the damaged PSII reaction center, thus positively regulating photosynthetic reaction and water-deficit tolerance in maize seedlings. Our data implied that SA played an important regulatory role in plant resistance to water-deficit stress, and the result will further supply the regulatory network of SA-mediated photosynthetic adaptability.

Leaf morphology is one of the important traits related to ideal plant architecture and is an important factor determining rice stress resistance, which directly affects yield. Wax layers form a barrier to protect plants from different environmental stresses. However, the regulatory effect of wax synthesis genes on leaf morphology and salt tolerance is not well-understood. In this study, we identified a rice mutant, leaf tip rumpled 1 (ltr1), in a mutant library of the classic japonica variety Nipponbare. Phenotypic investigation of NPB and ltr1 suggested that ltr1 showed rumpled leaf with uneven distribution of bulliform cells and sclerenchyma cells, and disordered vascular bundles. A decrease in seed-setting rate in ltr1 led to decreased per-plant grain yield. Moreover, ltr1 was sensitive to salt stress, and LTR1 was strongly induced by salt stress. Map-based cloning of LTR1 showed that there was a 2-bp deletion in the eighth exon of LOC_Os02g40784 in ltr1, resulting in a frameshift mutation and early termination of transcription. Subsequently, the candidate gene was confirmed using complementation, overexpression, and knockout analysis of LOC_Os02g40784. Functional analysis of LTR1 showed that it was a wax synthesis gene and constitutively expressed in entire tissues with higher relative expression level in leaves and panicles. Moreover, overexpression of LTR1 enhanced yield in rice and LTR1 positively regulates salt stress by affecting water and ion homeostasis. These results lay a theoretical foundation for exploring the molecular mechanism of leaf morphogenesis and stress response, providing a new potential strategy for stress-tolerance breeding.