Plant diseases, caused by a wide range of pathogens, severely reduce crop yield, quality and pose a threat to global food security. Developing broad-spectrum resistance (BSR) in crops is a key strategy to control crop diseases and safeguard crop production. Cloning of disease-resistance (R) genes and understanding their underlying molecular mechanisms provides new genetic resources and strategies for crop breeding. Novel genetic engineering and genome editing tools have accelerated the study of BSR genes and engineering of BSR in crops, and this area represents the primary focus of this review. We first summarize recent advances in the understanding of the plant immune system. We then examine progress in understanding molecular mechanisms underlying BSR in crops. Finally, we highlight diverse strategies employed to achieve BSR, such as gene stacking to combine multiple R genes, multiplexed genome editing of susceptibility (S) genes and promoters of executor R genes, editing cis-regulatory elements for fine-tuning gene expression, RNA interference, saturation mutagenesis, and precise genomic insertions. Genetic studies and engineering of BSR accelerate breeding of disease-resistant cultivars and crop improvement, which will act to safeguard global food security.

Genome-wide identification and comparative gene family analyses have been commonly performed to investigate species-specific evolution linked to various traits and molecular pathways. However, most previous studies were limited to gene screening in a single reference genome, failing to account for the gene presence/absence variations (gPAVs) in a species. Here, we propose an innovative pangenome-based approach of gene family analyses based on orthologous gene groups (OGGs). Using the basic helix-loop-helix (bHLH) transcription factor family in barley as an example, we identified 161 ∼ 176 bHLHs in 20 barley genomes, which could be classified into 201 OGGs. These 201 OGGs were further classified into 140 core, 12 soft-core, 29 shell, and 20 line-specific/cloud bHLHs, revealing a complete profile of bHLH in barley. Using a genome-scan approach, we overcome the genome annotation bias and identified on average 1.5 un-annotated core bHLHs per barley genome. We found that all core bHLHs belong to whole genome/segmental duplicates whilst dispensable bHLHs were more likely to result from small scale duplication events. Interestingly, we noticed that the dispensable bHLHs tended to enrich in specific subfamilies SF13, SF27, and SF28, implying the potential biased expansion of specific bHLHs in barley. We found that 50% of the bHLHs contain at least one intact transposon element within the 2kb upstream-to-downstream region. bHLHs with CNV have 1.48 TEs on average, significantly higher than 1.36 for core bHLH without CNV, supporting TEs’ potential role in bHLH expansion. Selection pressure analyses showed that dispensable bHLHs had experienced clear relaxed selection compared to core bHLHs, consistent with their conservation patterns. We further integrate pangenome with recently available barley pantranscriptome data in 5 tissues and discovered apparent transcriptional divergence within and across bHLH subfamilies. We conclude that pangenome-based gene family analyses can better describe the genuine evolution status of bHLHs untapped before and provided novel insights into bHLH evolution in barley. We expect this study will inspire similar analyses in many other gene families and species.

Brassinosteroids (BRs) are steroidal phytohormones indispensable for plant growth, development, and responses to environmental stresses. The export of bioactive BRs to the apoplast is essential for BR signalling initiation, which requires binding of BR molecule to the extracellular domains of the plasma membrane-localized receptor complex. We have previously shown that the Arabidopsis thaliana ATP-binding cassette (ABC) transporter, ABCB19, functions as a BR exporter, and together with its close homologue, ABCB1, positively regulate BR signalling. Here, we demonstrate that ABCB1 is another BR transporter. The ATP hydrolysis activity of ABCB1 was stimulated by bioactive BRs, and its transport activity was confirmed in proteoliposomes and protoplasts. Structures of ABCB1 in substrate-unbound (apo), brassinolide (BL)-bound, and ATP plus BL-bound states were determined. In the BL-bound structure, BL was bound to the hydrophobic cavity formed by the transmembrane domain, and triggered local conformational changes. Together, our data provide additional insights into the ABC transporter-mediated BR export.

Heterosis is extensively utilized in the two-line hybrid breeding system. Photo-/thermo-sensitive genic male sterile (P/TGMS) lines are key components of two-line hybrid rice. TGMS lines containing tms5 have significantly advanced two-line hybrid rice breeding. We cloned the TMS5 gene and found that TMS5 is a tRNA cyclic phosphatase that can remove 2',3'-cyclic phosphate (cP) from cP-ΔCCA-tRNAs for efficient repair to ensure maintenance of mature tRNA levels. tms5 mutation causes increased cP-ΔCCA-tRNAs and reduced mature tRNAs, leading to male sterility at the restrictive temperatures. However, the regulatory network of tms5-mediated TGMS remains to be elucidated. Here, we identified that an E3 ligase OsHel2 cooperates with TMS5 to regulate TGMS at the restrictive temperatures. Consistently, both the accumulation of 2',3'-cP-ΔCCA-tRNAs and insufficiency of mature tRNAs in tms5 mutant were largely recovered in the tms5 oshel2-1 mutant. A lesion in OsHel2 results in partial readthrough of the stalled sequences, thereby evading ribosome-associated protein quality control (RQC) surveillance. Our findings reveal a mechanism by which the OsHel2 impede readthrough of stalled mRNA sequences to regulate male fertility in TGMS rice, thus providing a paradigm for investigating how disorders in the components of the RQC pathway impair cellular functions and lead to diseases or defects in other organisms.

The introduction of Reduced height (Rht) genes into wheat varieties results in semidwarf plant architecture with largely improved lodging resistance and harvest indices. Therefore, the exploration of new Rht gene resources to breed semidwarf wheat cultivars has been a major strategy for guaranteeing high and stable grain yields of wheat since the 1960s. In this study, we report the map-based cloning of TaERF-A1, which encodes an AP2/ERF transcription factor and acts as a positive regulator of wheat stem elongation, as a new gene for regulating plant height and spike length. The natural variant TaERF-A1JD6, characterized by a substitution from Phe (derived from Nongda3338) to Ser (derived from Jingdong6) at position 178, significantly weakened the stability of the TaERF-A1 protein. As a result, this substitution led to partly attenuated transcriptional activation of TaERF-A1-targeted downstream genes, including TaPIF4, resulting in the restriction of stem and spike elongation. Importantly, introgression of the semidwarfing-related allele TaERF-A1JD6 in wheat materials significantly enhanced lodging resistance, especially in dense cropping systems. Therefore, our study reveals TaERF-A1JD6 as a new Rht gene resource for breeding semidwarf wheat varieties with increased yield stability.