Publications

Polyploid crops such as wheat, Brassica and cotton are critical in global agricultural and economic system. However, their productivity is threatened increasingly by biotic stresses such as disease, and abiotic stresses such as heat, both exacerbated by climate change. Understanding the molecular basis of stress responses in these crops is crucial but remains challenging due to their complex genetic makeup—characterized by large sizes, multiple genomes and limited annotation resources. Proteomics is a powerful approach to elucidate molecular mechanisms, enabling the identification of stress-responsive proteins, cellular localization, physiological, biochemical and meta-bolic pathways, protein-protein interactions, and post-translational modifications. It also sheds light on the evolutionary consequences of genome duplication and hybridi-zation. Breeders can improve stress tolerance and yield traits by characterizing the proteome of polyploid crops. Functional and subcellular proteomics, and the identifi-cation and introgression of stress-responsive protein biomarkers, are promising for crop improvement. Nonetheless, several challenges remain, including inefficient pro-tein extraction method, limited organelle-specific data, insufficient protein annota-tions, low proteoform coverage, reproducibility and lack of target-specific antibodies. This review explores the genomic complexity of three key allopolyploid crops—wheat, oilseed Brassica, and cotton—summarizes recent proteomic insights into heat stress and pathogen response and discusses current challenges and future directions for ad-vancing proteomics in polyploid crop improvement through proteomics.

ABSTRACT Climate warming and nitrogen deposition—two key drivers of global change—significantly influence soil multifunctionality and microbial community dynamics. Biocrusts are crucial in mitigating these impacts and supporting soil ecological functions and biodiversity. However, how soil multifunctionality and microbial communities within different biocrusts respond to these drivers—and the mechanisms involved—remains unclear. This study explores the effects of warming and nitrogen addition on soil multifunctionality and bacterial communities in cyanobacterial and moss crusts in the Mu Us Sandland. Using Partial Least Squares Structural Equation Modelling, we identified the pathways through which these global change factors influence soil multifunctionality. Our results show that warming and nitrogen addition exert significant yet contrasting effects on soil multifunctionality and bacterial community structure, varying markedly between biocrust types. Specifically, warming enhanced soil multifunctionality in moss crusts but reduced it in cyanobacterial crusts. Combined warming and nitrogen addition significantly decreased bacterial alpha diversity in moss crusts, while cyanobacterial crusts were relatively unresponsive. Moreover, key bacterial phyla—particularly Proteobacteria and Bacteroidetes—mediated the effects of warming and nitrogen addition through changes in their relative abundances, exerting negative and positive influences on multifunctionality in cyanobacterial and moss crusts, respectively. This study underscores the capacity of moss crusts to maintain soil multifunctionality under global change conditions and reveals a key mechanism by which shifts in dominant bacterial phyla mediate biocrust responses to environmental stressors.

Soil bacteria and fungi play key roles in organic matter decomposition and nutrient turnover. Aerated drip irrigation (ADI) is beneficial for improving soil nutrients but its effects on bacterial and fungal communities are less known. In this study, a two-season ADI field experiment comprising three dissolved oxygen concentrations (10, 15, and 20 mg·L–1, referred to as A1, A2, and A3) and a control treatment (groundwater without aerated, CK) was conducted in a tomato plantation in Shandong, China. Soil bacterial and fungal communities were examined using high-throughput sequencing targeting 16 S rRNA and ITS genes, respectively. The ADI treatments increased fungal community diversity but did not significantly affect bacterial community diversity. However, bacterial communities were more connected within the module, with more stable network structures in the ADI treatments. In contrast, fungal networks had lower modularity values and a significant negative correlation with soil available phosphorus (AP). The ADI treatments increased the bacterial phylum Gemmatimonadetes and Firmicutes and a few aerobic taxa and strongly enriched the fungal phylum Mortierellomycota and phosphorus-dissolving taxa (Humicola, Mycothermus, and Myceliophthora). In addition, the A2 treatment enhanced functional groups related to carbon and phosphorus cycling while decreasing Plant Pathogen functional groups. The most important environmental factors affecting bacterial and fungal communities were soil organic carbon (SOC) and AP, respectively. Structural equation modeling (SEM) demonstrated that ADI directly affected soil bacterial and fungal communities and indirectly promoted SOC, AP content, and tomato yield. Overall, our findings highlight the importance of bacterial and fungal taxonomic communities, co-occurrence networks, and functions related to regulating soil carbon and phosphorus availability, providing novel evidence for the application of ADI to improve soil fertility and crop productivity.

Global food production faces challenges in balancing the need for increased yields with environmental sustainability. This study presents a six-year field experiment in the North China Plain, demonstrating the benefits of diversifying traditional cereal monoculture (wheat-maize) with cash crops (sweet potato) and legumes (peanut and soybean). The diversified rotations increase equivalent yield by up to 38%, reduce N₂O emissions by 39%, and improve the system's greenhouse gas balance by 88%. Furthermore, including legumes in crop rotations stimulates soil microbial activities, increases soil organic carbon stocks by 8%, and enhances soil health (indexed with the selected soil physiochemical and biological properties) by 45%. The large-scale adoption of diversified cropping systems in the North China Plain could increase cereal production by 32% when wheat-maize follows alternative crops in rotation and farmer income by 20% while benefiting the environment. This study provides an example of sustainable food production practices, emphasizing the significance of crop diversification for long-term agricultural resilience and soil health.

Chickpea (Cicer arietinum L.) is an important legume crop that has been subjected to intensive breeding, resulting in limited genetic diversity. Australia is the world's second largest producer and the leading exporter of chickpea; the genomic architecture of its cultivars remains largely unexplored. This knowledge gap hinders efforts to enhance their genetic potential for production, protection, and stress adaptation. To address this, we generated high-quality genome assemblies and annotations for 15 leading Australian chickpea cultivars using single-tube long-fragment read technology. The pan-genome analysis identified 34 345 gene families, including 13 986 dispensable families enriched for genes associated with key agronomic traits. Comparative genomic analysis revealed ~2.5 million single-nucleotide polymorphisms, nearly 200 000 insertions/deletions, and over 280 000 structural variations. These variations were found in key flowering time genes, seed weight-related genes, and disease resistance genes, providing insights into the genetic diversity underlying these critical traits. Haplotype analysis of key genes within the 'QTL-hotspot' region revealed the absence of superior haplotypes in Australian cultivars. Validation using Kompetitive allele-specific PCR markers confirmed these findings, highlighting the need to introduce beneficial haplotypes from diverse accessions to enhance drought tolerance in Australian chickpea cultivars. The genomic resources generated in this study provide valuable insights into chickpea genetic diversity and offer potential avenues for crop improvement.

The arbuscular mycorrhizal (AM) fungal symbiosis offers a transformative solution to mitigate agroecosystem challenges linked to the excessive use of synthetic chemicals. However, the role of AM-plant communication in response to anthropogenic activities and hyphal network functionality remains poorly understood. Here, we reposition AM fungal hyphosphere networks as a keystone ecological infrastructure for sustainable agroecosystems. Drawing on a synthesis of thousands of global experimental studies, we highlight the primary environmental functions of AM fungus-plant communication: enhancing agroecosystem resilience by buffering crops against diverse biotic and abiotic stressors through molecular signaling and physiological modulation, mediating energy transfer via small-RNA-mediated cross-kingdom interactions, facilitating hydraulic redistribution within the soil profile through hyphospheric networks, and optimizing root architecture via effective colonization for improved nutrient acquisition. Certain anthropogenic practices-such as soil disturbance, non-mycorrhizal crop monoculture, and fungicide application-can disrupt AM hyphal networks; however, these impacts can be minimized through improved farming practices, such as cropping diversification with legumes and AM fungus-compatible crops, AM-responsive plant genotypes, effective AM fungal inoculation, and microbial consortium amendments. Integrating insights into AM fungal mechanisms with anthropogenic practices and policy support is essential to scaling AM benefits across ecoregions. Harnessing AM fungal functionality can increase nutrient use efficiency, reduce reliance on chemical inputs, and enhance ecosystem productivity, offering a microbe-centered blueprint to support the United Nations' sustainability goals.