Genomics-based strategies for the use of natural variation in the improvement of crop metabolism

Scossa, Federico; Brotman, Yariv; Lima, Francisco de Abreu e; Willmitzer, Lothar; Nikoloski, Zoran; Tohge, Takayuki; Fernie, Alisdair R.

doi:10.1016/j.plantsci.2015.05.021

Cited by 63 publications

(34 citation statements)

References 250 publications

(187 reference statements)

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“…The crop yield and the quality of produce depend on the quantity of metabolites produced by the plant. Metabolites play an important role in plant development and respond to diverse environmental conditions (Scossa et al, 2016). Begomovirus infection in host plants triggers an array of morphological, biochemical and molecular changes (Mandadi and Scholthof, 2013).…”

Section: Introductionmentioning

confidence: 99%

Ageratum enation virus Infection Induces Programmed Cell Death and Alters Metabolite Biosynthesis in Papaver somniferum

et al. 2017

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A previously unknown disease which causes severe vein thickening and inward leaf curl was observed in a number of opium poppy (Papaver somniferum L.) plants. The sequence analysis of full-length viral genome and associated betasatellite reveals the occurrence of Ageratum enation virus (AEV) and Ageratum leaf curl betasatellite (ALCB), respectively. Co-infiltration of cloned agroinfectious DNAs of AEV and ALCB induces the leaf curl and vein thickening symptoms as were observed naturally. Infectivity assay confirmed this complex as the cause of disease and also satisfied the Koch’s postulates. Comprehensive microscopic analysis of infiltrated plants reveals severe structural anomalies in leaf and stem tissues represented by unorganized cell architecture and vascular bundles. Moreover, the characteristic blebs and membranous vesicles formed due to the virus-induced disintegration of the plasma membrane and intracellular organelles were also present. An accelerated nuclear DNA fragmentation was observed by Comet assay and confirmed by TUNEL and Hoechst dye staining assays suggesting virus-induced programmed cell death. Virus-infection altered the biosynthesis of several important metabolites. The biosynthesis potential of morphine, thebaine, codeine, and papaverine alkaloids reduced significantly in infected plants except for noscapine whose biosynthesis was comparatively enhanced. The expression analysis of corresponding alkaloid pathway genes by real time-PCR corroborated well with the results of HPLC analysis for alkaloid perturbations. The changes in the metabolite and alkaloid contents affect the commercial value of the poppy plants.

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Section: Introductionmentioning

confidence: 99%

Ageratum enation virus Infection Induces Programmed Cell Death and Alters Metabolite Biosynthesis in Papaver somniferum

et al. 2017

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“…For this reason, the quantitative trait loci approach is a powerful alternative method of associating phenotypes to their underlying genetic variance. The use of such approaches in plant metabolism has been the subject of several recent comprehensive reviews (Kliebenstein, 2009;Scossa et al, 2015); however, we will provide a couple of examples of their utility for advancing the understanding of metabolite accumulation and metabolic regulation.…”

Section: Integrating Metabolite and Genome Datamentioning

confidence: 99%

Integrative Approaches to Enhance Understanding of Plant Metabolic Pathway Structure and Regulation

2015

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Huge insight into molecular mechanisms and biological network coordination have been achieved following the application of various profiling technologies. Our knowledge of how the different molecular entities of the cell interact with one another suggests that, nevertheless, integration of data from different techniques could drive a more comprehensive understanding of the data emanating from different techniques. Here, we provide an overview of how such data integration is being used to aid the understanding of metabolic pathway structure and regulation. We choose to focus on the pairwise integration of large-scale metabolite data with that of the transcriptomic, proteomics, whole-genome sequence, growth-and yield-associated phenotypes, and archival functional genomic data sets. In doing so, we attempt to provide an update on approaches that integrate data obtained at different levels to reach a better understanding of either single gene function or metabolic pathway structure and regulation within the context of a broader biological process.

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“…While both the extent of allelic diversity and the density of recombination break points can be enhanced through the construction of multiparent advanced generation intercross populations (Balasubramanian et al, 2009;Kover et al, 2009), the resulting mapping populations from such a time-consuming effort would not reflect the frequencies and combinations of alleles found in the natural population (Weigel, 2012). In recent years, a number of genome-wide association studies (GWAS) have exploited historical recombination events in large association panels of unrelated individuals assembled to capture the phenotypic variability of a wide range of complex traits, allowing it to offer higher mapping resolution of causal loci (Atwell et al, 2010;Huang et al, 2011;Li et al, 2012;Ramstein et al, 2015;Scossa et al, 2016). Although it has its own set of limitations, such as possible spurious associations due to cryptic population structure and multiple levels of relatedness, GWAS often overcomes the two major weaknesses inherent to QTL detection in RIL populations (Pritchard and Donnelly, 2001;Yu and Buckler, 2006;Platt et al, 2010aPlatt et al, , 2010bTrontin et al, 2011;Korte and Farlow, 2013).…”

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Network-Guided GWAS Improves Identification of Genes Affecting Free Amino Acids

et al. 2016

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Amino acids are essential for proper growth and development in plants. Amino acids serve as building blocks for proteins but also are important for responses to stress and the biosynthesis of numerous essential compounds. In seed, the pool of free amino acids (FAAs) also contributes to alternative energy, desiccation, and seed vigor; thus, manipulating FAA levels can significantly impact a seed's nutritional qualities. While genome-wide association studies (GWAS) on branched-chain amino acids have identified some regulatory genes controlling seed FAAs, the genetic regulation of FAA levels, composition, and homeostasis in seeds remains mostly unresolved. Hence, we performed GWAS on 18 FAAs from a 313-ecotype Arabidopsis (Arabidopsis thaliana) association panel. Specifically, GWAS was performed on 98 traits derived from known amino acid metabolic pathways (approach 1) and then on 92 traits generated from an unbiased correlation-based metabolic network analysis (approach 2), and the results were compared. The latter approach facilitated the discovery of additional novel metabolic interactions and singlenucleotide polymorphism-trait associations not identified by the former approach. The most prominent network-guided GWAS signal was for a histidine (His)-related trait in a region containing two genes: a cationic amino acid transporter (CAT4) and a polynucleotide phosphorylase resistant to inhibition with fosmidomycin. A reverse genetics approach confirmed CAT4 to be responsible for the natural variation of His-related traits across the association panel. Given that His is a semiessential amino acid and a potent metal chelator, CAT4 orthologs could be considered as candidate genes for seed quality biofortification in crop plants.Free amino acids (FAAs) play a pivotal role in the central metabolism of plants. FAAs serve as building blocks for protein synthesis and also are precursors for osmolytes, alternative energy, hormones, and key secondary metabolites (Rai, 2002; Araújo et al., 2010;Tzin and Galili, 2010; Angelovici et al., 2011). Studies of both developing and germinating seeds also have implicated FAAs in proper seed development and germination (Angelovici et al., 2010;Galili and Amir, 2013). Still, the genetic control of FAA metabolism in seed remains poorly understood. One reason is that FAA metabolism is tightly intertwined with essential cellular processes in plants, and manipulating FAA levels can have strong deleterious, pleiotropic effects on the entire system (Guyer et al., 1995;Galili, 2011;Ingle, 2011;Pratelli and Pilot, 2014). For example, increasing Lys and Thr inhibits the activity of Asp kinase via a feedback inhibition loop (Clark and Lu, 2015). At high concentrations, this inhibition can lead to starvation of a downstream metabolic product, Met, which inhibits plant growth (Bright et al., 1982;Rognes et al., 1983;Heremans and Jacobs, 1995). In addition, several amino acid catabolic products, such as those emanating from branched-chain amino acids (BCAAs) or Lys degradation pathways, can be chan...

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Genomics-based strategies for the use of natural variation in the improvement of crop metabolism

Cited by 63 publications

References 250 publications

Ageratum enation virus Infection Induces Programmed Cell Death and Alters Metabolite Biosynthesis in Papaver somniferum

Ageratum enation virus Infection Induces Programmed Cell Death and Alters Metabolite Biosynthesis in Papaver somniferum

Integrative Approaches to Enhance Understanding of Plant Metabolic Pathway Structure and Regulation

Network-Guided GWAS Improves Identification of Genes Affecting Free Amino Acids

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