Single pathogen‐targeted disease management measure has shown drawbacks in field efficacy under the scenario of global change. An in‐depth understanding of plant pathogenesis will provide a promising solution but faces the challenges of the emerging paradigm involving the plant microbiome. While the beneficial impact of the plant microbiome is well characterized, their potential role in facilitating pathological processes has so far remained largely overlooked. To address these unsolved controversies and emerging challenges, we hereby highlight the pathobiome, the disease‐assisting portion hidden in the plant microbiome, in the plant pathogenesis paradigm. We review the detrimental actions mediated by the pathobiome at multiple scales and further discuss how natural and human triggers result in the prevalence of the plant pathobiome, which would probably provide a clue to the mitigation of plant disease epidemics. Collectively, the article would advance the current insight into plant pathogenesis and also pave a new way to cope with the upward trends of plant disease by designing the pathobiome‐targeted measure.

Summary: Submergence tolerance is crucial for the direct seeding of rice, yet long‐term domestication and breeding have inadvertently reduced the adaptability of cultivated rice to submergence stress. Here, we identify a nucleic acid excision repair protein‐encoding gene qSHS5 as an essential regulator of seedling height under submergence through a genome‐wide association study in 322 rice accessions. Disruption of qSHS5 in mutants resulted in seedling growth inhibition under submergence, while growth remains comparable to wild‐type under normal conditions. This inhibition is primarily due to decreased cell number resulting from G1 phase cell cycle arrest. Further investigation showed that levels of reactive oxygen species (ROS), O₂⁻ and H₂O₂ significantly increased, and DNA damage was aggravated in qshs5 mutants under submergence. Additionally, we find the submergence‐tolerant haplotype qSHS5^H4 has been progressively lost, while the elite haplotype qSHS5^H3 has been largely overlooked during the breeding of semi‐dwarf and high‐yield in rice. Importantly, we demonstrate that combining qSHS5^H3 with the semi‐dwarfing haplotype SD1^H1 exhibited high yield without compromising submergence tolerance, offering significant potential for future breeding programmes targeting direct seeding cultivation. This study not only identifies a novel superior allele but also provides valuable insights for future improvement of rice cultivation, particularly under climate change‐induced submergence for direct seeding.

Background: CCCH zinc finger proteins (OsC3Hs) are a class of transcriptional regulators that play important roles in plant development and stress responses. Although their functional significance has been widely studied in model species, comprehensive genome-wide characterization of CCCH proteins in rice (Oryza sativa) remains limited. Methods: Using Arabidopsis CCCH proteins as references, we identified the CCCH gene family in rice and analyzed the physicochemical properties, subcellular localization, conserved structures, phylogeny, cis-regulatory elements, synteny analysis, spatiotemporal expression patterns, and expression patterns under drought, ABA, and MeJA treatments for the identified CCCH family members. Results: The results showed that the rice CCCH family comprises 73 members, which are unevenly distributed across the 12 chromosomes. Phylogenetic analysis classified them into 11 subfamilies. Subcellular localization indicated that most members are localized in the nucleus. The upstream regions of CCCH promoters contain a large number of cis-regulatory elements related to plant hormones and biotic stress responses. Most genes respond to drought, abscisic acid (ABA), and methyl jasmonate (MeJA) treatments. OsC3H36 was highly expressed under drought, ABA, and MeJA treatments. Haplotype analysis of this gene revealed two major allelic variants (H1 and H2), with H1 predominantly found in japonica rice and associated with increased grain width and 1000-grain weight. Functional validation using a chromosome segment substitution line (CSSL1) confirmed these findings. Conclusions: CCCH genes play important roles in rice growth, development, and stress responses. Additionally, we validated that OsC3H36 is associated with rice grain width and 1000-grain weight.