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  • | 18 Mar 2022 | OPEN

    Genomic structural variation in tomato and its role in plant immunity

    Emma Jobson and Robyn Roberts✉

     

    Abstract

    It is well known that large genomic variations can greatly impact the phenotype of an organism. Structural Variants (SVs) encompass any genomic variation larger than 30 base pairs, and include changes caused by deletions, inversions, duplications, transversions, and other genome modifications. Due to their size and complex nature, until recently, it has been difficult to truly capture these variations. Recent advances in sequencing technology and computational analyses now permit more extensive studies of SVs in plant genomes. In tomato, advances in sequencing technology have allowed researchers to sequence hundreds of genomes from tomatoes, and tomato relatives. These studies have identified SVs related to fruit size and flavor, as well as plant disease response, resistance/susceptibility, and the ability of plants to detect pathogens (immunity). In this review, we discuss the implications for genomic structural variation in plants with a focus on its role in tomato immunity. We also discuss how advances in sequencing technology have led to new discoveries of SVs in more complex genomes, the current evidence for the role of SVs in biotic and abiotic stress responses, and the outlook for genetic modification of SVs to advance plant breeding objectives.

  • | 18 Mar 2022 | OPEN

    Molecular and biochemical basis of softening in tomato

    Duoduo Wang and Graham B. Seymour✉

     

    Abstract

    We review the latest information related to the control of fruit softening in tomato and where relevant compare the events with texture changes in other fleshy fruits. Development of an acceptable texture is essential for consumer acceptance, but also determines the postharvest life of fruits. The complex modern supply chain demands effective control of shelf life in tomato without compromising colour and flavour. The control of softening and ripening in tomato (Solanum lycopersicum) are discussed with respect to hormonal cues, epigenetic regulation and transcriptional modulation of cell wall structure-related genes. In the last section we focus on the biochemical changes closely linked with softening in tomato including key aspects of cell wall disassembly. Some important elements of the softening process have been identified, but our understanding of the mechanistic basis of the process in tomato and other fruits remains incomplete, especially the precise relationship between changes in cell wall structure and alterations in fruit texture.

  • | 18 Mar 2022 | OPEN

    Resequencing and genome-wide association studies of autotetraploid potato

    Feng Zhang, Li Qu, Yincong Gu, Zhi-Hong Xu and Hong-Wei Xue✉

     

    Abstract

    Potato is the fourth most important food crop in the world. Although with a long history for breeding approaches, genomic information and association between genes and agronomic traits remain largely unknown particularly in autotetraploid potato cultivars, which limit the molecular breeding progression. By resequencing the genome of 108 main cultivar potato accessions with rich genetic diversity and population structure from International Potato Center, with approximate 20-fold coverage, we revealed more than 27 million Single Nucleotide Polymorphisms and ~ 3 million Insertion and Deletions with high quality and accuracy. Domestication analysis and genome-wide association studies (GWAS) identified candidate loci related to photoperiodic flowering time and temperature sensitivity as well as disease resistance, providing informative insights into the selection and domestication of cultivar potato. In addition, GWAS with GWASploy for 25 agronomic traits identified candidate loci by association signals, especially those related to tuber size, small-sized tuber weight and tuber thickness that was also validated by transcriptome analysis. Our study provides a valuable resource that facilitates the elucidation of domestication process as well as the genetic studies and agronomic improvement of autotetraploid potato.

Most Accessed
  • | 18 Mar 2022 | OPEN

    The leaf senescence-promoting transcription factor AtNAP activates its direct target gene CYTOKININ OXIDASE 3 to facilitate senesc...

    Youzhen Hu, Bin Liu, Huazhong Ren, Liping Chen, Christopher B. Watkins and Su-Sheng Gan✉

     

    Core

    Cytokinins retard leaf senescence and must be degraded at the onset of and during leaf senescence. A mechanism is revealed, in which the senescence-specific transcription factor, AtNAP, physically binds to the promoter of AtCKX3 to activate cytokinin oxidase expression and catabolizing cytokinins and thereby facilitating senescence processes.

  • | 08 Sep 2021 | OPEN

    Genetic characterization of melon accessions in the U.S. National Plant Germplasm System and construction of a melon core collecti...

    Xin Wang, Kaori Ando, Shan Wu, Umesh K. Reddy, Prabin Tamang, Kan Bao, Sue A. Hammar, Rebecca Grumet, James D. McCreight✉ and Zhangjun Fei✉

     

    Core

    Genetic characterization of 2083 melon accessions in the U.S. National Plant Germplasm System provides insights into melon genetic diversity, origin and domestication, and facilitates the construction of a melon core collection that captures the majority of the genetic variation in the germplasm. Genome-wide association studies identified potentially associated genome regions related to fruit quality and other horticultural traits, providing valuable information for melon research and breeding.

  • | 05 Sep 2021 | OPEN

    Multiple functions of the vacuole in plant growth and fruit quality

    Yu-Tong Jiang, Lu-Han Yang, Ali Ferjani and Wen-Hui Lin✉

     

    Abstract

    Vacuoles are organelles in plant cells that play pivotal roles in growth and developmental regulation. The main functions of vacuoles include maintaining cell acidity and turgor pressure, regulating the storage and transport of substances, controlling the transport and localization of key proteins through the endocytic and lysosomal-vacuolar transport pathways, and responding to biotic and abiotic stresses. Further, proteins localized either in the tonoplast (vacuolar membrane) or inside the vacuole lumen are critical for fruit quality. In this review, we summarize and discuss some of the emerging functions and regulatory mechanisms associated with plant vacuoles, including vacuole biogenesis, vacuole functions in plant growth and development, fruit quality, and plant-microbe interaction, as well as some innovative research technology that has driven advances in the field. Together, the functions of plant vacuoles are important for plant growth and fruit quality. The investigation of vacuole functions in plants is of great scientific significance and has potential applications in agriculture.

  • | 05 Sep 2021 | OPEN

    Leaf senescence: progression, regulation, and application

    Yongfeng Guo, Guodong Ren, Kewei Zhang, Zhonghai Li, Ying Miao✉ and Hongwei Guo✉

     

    Abstract

    Leaf senescence, the last stage of leaf development, is a type of postmitotic senescence and is characterized by the functional transition from nutrient assimilation to nutrient remobilization which is essential for plants’ fitness. The initiation and progression of leaf senescence are regulated by a variety of internal and external factors such as age, phytohormones, and environmental stresses. Significant breakthroughs in dissecting the molecular mechanisms underpinning leaf senescence have benefited from the identification of senescence-altered mutants through forward genetic screening and functional assessment of hundreds of senescence-associated genes (SAGsvia reverse genetic research in model plant Arabidopsis thaliana as well as in crop plants. Leaf senescence involves highly complex genetic programs that are tightly tuned by multiple layers of regulation, including chromatin and transcription regulation, post-transcriptional, translational and post-translational regulation. Due to the significant impact of leaf senescence on photosynthesis, nutrient remobilization, stress responses, and productivity, much effort has been made in devising strategies based on known senescence regulatory mechanisms to manipulate the initiation and progression of leaf senescence, aiming for higher yield, better quality, or improved horticultural performance in crop plants. This review aims to provide an overview of leaf senescence and discuss recent advances in multi-dimensional regulation of leaf senescence from genetic and molecular network perspectives. We also put forward the key issues that need to be addressed, including the nature of leaf age, functional stay-green trait, coordination between different regulatory pathways, source-sink relationship and nutrient remobilization, as well as translational researches on leaf senescence.

  • | 05 Sep 2021 | OPEN

    Genome-wide binding analysis of the tomato transcription factor SlDof1 reveals its regulatory impacts on fruit ripening

    Yuying Wang, Peiwen Wang, Weihao Wang, Lingxi Kong, Shiping Tian and Guozheng Qin✉

     

    Core

    The transcription factor SlDof1 is required for normal fruit ripening in tomato. Knockdown of SlDof1 expression delays ripening-related processes, and transcriptome analysis coupled with ChIP-seq shows that some well-known ripening-related genes are direct targets of SlDof1. Our study demonstrates SlDof1’s regulatory function and provides insights about the molecular regulatory networks controlling fruit ripening.