Modern potato breeding methods following a genomic-led approach provide means for shortening breeding cycles and increasing breeding efficiency across selection cycles. Acquiring genetic data for ...large breeding populations remains expensive. We present a pipeline to reduce the number of single nucleotide polymorphisms (SNPs) to lower the cost of genotyping. First, we reduced the number of individuals to be genotyped with a high-throughput method according to the multi-trait variation as defined by principal component analysis of phenotypic characteristics. Next, we reduced the number of SNPs by pruning for linkage disequilibrium. By adjusting the square of the correlation coefficient between two adjacent loci, we obtained reduced subsets of SNPs. We subsequently tested these SNP subsets by two methods; (1) a genome-wide association study (GWAS) for marker identification, and (2) genomic selection (GS) to predict genomic estimated breeding values. The results indicate that both GWAS and GS can be done without loss of information after SNP reduction. The pipeline allows for creating custom SNP subsets to cover all variation found in any particular breeding population. Low-throughput genotyping will reduce the genotyping cost associated with large populations, thereby making genomic breeding methods applicable to large potato breeding populations by reducing genotyping costs.
Cytokinins are plant hormones that typically block or delay leaf senescence. We profiled 34 different cytokinins/cytokinin metabolites (including precursors, conjugates and degradation products) in ...leaves of a free‐growing mature aspen (Populus tremula) before and after the initiation of autumnal senescence over three consecutive years. The levels and profiles of individual cytokinin species, or classes/groups, varied greatly between years, despite the fact that the onset of autumn senescence was at the same time each year, and senescence was not associated with depletion of either active or total cytokinin levels. Levels of aromatic cytokinins (topolins) were low and changed little over the autumn period. Diurnal variations and weather‐dependent variations in cytokinin content were relatively limited. We also followed the expression patterns of all aspen genes implicated as having roles in cytokinin metabolism or signalling, but neither the pattern of regulation of any group of genes nor the expression of any particular gene supported the notion that decreased cytokinin signalling could explain the onset of senescence. Based on the results from this tree, we therefore suggest that cytokinin depletion is unlikely to explain the onset of autumn leaf senescence in aspen.
We profiled cytokinins/cytokinin metabolites in leaves of an aspen (Populus tremula) before and after the initiation of autumnal senescence over 3 years. The levels and profiles varied greatly between years, despite the fact that the onset of autumn senescence was at the same time. No pattern of pattern of gene expression supported the notion that decreased cytokinin signalling could explain the onset of senescence, and we suggest that cytokinin depletion is unlikely to explain the onset of autumn leaf senescence in aspen.
Atractylodes lancea
(Thunb.) DC. is a well-known medicinal herb in China, containing abundant active components, including a variety of sesquiterpenoids. Owing to a shortage of wild resources, ...artificial cultivation has become the main breeding mode, leading to the germplasm degradation. In preliminary research, our research group found that a mutant tissue culture seedling of
A. lancea
is an excellent germplasm resource, characterized by early stem growth and higher sesquiterpenoid content than that of the wild type. In this study, the physiological and biochemical mechanisms underlying efficient sesquiterpenoids synthesis by this mutant
A. lancea
were systematically evaluated. The results showed that the photosynthetic efficiency, central carbon metabolism efficiency, and energy metabolism efficiency were significantly improved in mutant
A. lancea
compared with the wild type, and the content of endogenous hormones, such as gibberellin and jasmonic acid, changed significantly. In addition, levels of key metabolites and the expression level of key genes in the mevalonate and 2-C-methyl-
d
-erythritol-4-phosphate pathways were significantly higher in mutant type than in wild type, resulting in elevated sesquiterpenoid synthesis in the mutant. These physiological and biochemical properties explain the rapid growth and high sesquiterpenoid content of mutant
A. lancea
.
Key message
Efficient sesquiterpenoids synthesis in early stem growth mutation of
Atractylodes lancea
could be explained by the biological activities enhancement and up-regulation of sesquiterpene synthesis pathway via gibberellin and jasmonic acid.
Improved plants are necessary to meet human needs. Agrobacterium-mediated transformation is the most common method used to rewire plant capabilities. For plant gene delivery, DNA constructs are ...assembled into binary T-DNA vectors that rely on broad host range origins for bacterial replication. Here we present pLX vectors, a set of mini binary T-DNA plasmids suitable for Type IIS restriction endonuclease- and overlap-based assembly methods. pLX vectors include replicons from compatible broad host range plasmids. Simultaneous usage of pBBR1- and RK2-based pLX vectors in a two-plasmid/one-Agrobacterium strain strategy allowed multigene delivery to plants. Adoption of pLX vectors will facilitate routine plant transformations and targeted mutagenesis, as well as complex part and circuit characterization.
Editorial on the Research Topic Leeway to Operate With Plant Genetic Resources Different legal frameworks are applicable to the use of genetic resources (GR). These can broadly be categorized into ...(1) access and benefit-sharing (ABS), (2) biosafety aspects related to the technologies for improving the genetic material, and (3) intellectual property (IP) systems including plant variety rights (PVR) and patents specific to the plant innovation sector. With scientific and technical progress in research and breeding, as well as expanding internationalization, legal frameworks have become increasingly complex in the past few decades. In this context, the Research Topic “Leeway to operate with plant genetic resources” addresses the latest and most pertinent legalissues related to the use of GR in plant research and breeding.The contributions are summarized here and put into the larger societal and legal context that modern-day plant geneticists are facing.
While plant-based transient expression systems have demonstrated their potency to rapidly express economically feasible quantities of complex human proteins, less is known about their compatibility ...with posttranslational modification control. Here we investigated three commonly used transient expression vectors, pEAQ, magnICON and pTra for their capability to express a multi-component protein with controlled and modified N-glycosylation. Cetuximab (Cx), a therapeutic IgG1 monoclonal antibody, which carries next to the conserved Fc an additional N-glycosylation site (GS) in the Fab-domain, was used as model. While pEAQ and pTra produce fully assembled Cx at similar levels in
, the yield of magnICON-Cx was twice as high. When expressed in wild type plants, both Cx-GSs exhibited typical plant N-glycans decorated with plant-specific xylose and fucose. Likewise, Cx generated in the glycoengineered ΔXTFT line carried mainly complex N-glycans lacking plant specific residues. Exposure to different engineering settings (encompassing stable lines and transient approaches) towards human galactosylation and sialylation resulted in Cx carrying targeted N-glycans at similar quantities using all three expression vectors. Collectively, our results exhibit the universal application of plant-based glycoengineering, thereby increasing the attractivity of the ambitious expression platform.
Bioreactors provide suitable conditions for the growth of cells and production of secondary metabolites by regulating physical and chemical factors. In this study, saffron cell growth and the ...production of crocin metabolite were evaluated in Erlenmeyer flask and in a stirred bioreactor. To optimize the conditions, the effect of different concentrations of 2-(N-morpholino) ethanesulfonic acid (MES) (0, 2.5 and 5 mM) as a buffering agent and sucrose (3%, 6% and gradually 6%) were addressed on saffron cell growth and crocin production in the Erlenmeyer flask. This aim was then pursued in a stirred bioreactor through investigation on the effect of aeration and pH medium adjustment. The results of the first step experiment showed that Schenk and Hildebrandt basal medium with naphthalene acetic acid (2 mg l
−1
) and 6-benzylaminopurine (1 mg l
−1
) supplemented with 2.5 mM of MES as well as gradual increment of sucrose from 3 to 6% caused the highest cell biomass and crocin production. The spectrophotometry measurement showed that the highest crocin content of the cells was 0.8 mg g
−1
after 6 weeks. The results of the second part revealed that in the stirred bioreactor, constant pH (5.8) during the growth period is a limiting factor for the cell growth and crocin production. Aeration was also found to be an inhibiting factor for the production of crocin. The results showed that, if the evaporated volume of water caused by aeration is constituted, it can be an effective factor to increase cell growth around 2 folds. In addition, total crocin content of the proliferated cells in stirred bioreactor system under the non-constant pH and without aeration conditions, could be raised up to 2 mg g
−1
of cell dry weight, based on the HPLC determination. According to the results of this study, it can be concluded that MES and gradual increment of sucrose could increase the cell growth and crocin production. In the tested stirred bioreactor, it was found that the natural pH fluctuation is a suitable condition for saffron biomass cell growth and crocin production. The proper aeration could increase the cell biomass, if the evaporated water is replaced. However based on the obtained results it can be concluded that, aeration at tested value is not capable of increasing the crocin production.
Key message
Saffron, the most expensive spice contains valuable compounds like crocin. Corm derived-cell containing crocin can be produced in higher scales and cheaper price by using cell culture in stirred bioreactor.
NMR-based metabolic profiling of polar extracts of somatic embryogenic and organogenic cultures of the medicinal plant
Cymbopogon schoenanthus
subsp.
proximus
were studied. Regeneration through ...somatic embryogenesis was done on media containing 2,4-D and BAP while organogenesis was achieved on media containing NAA and BAP. Fifty-two metabolites were identified in embryogenic calli (EC), organogenic calli (OC), regenerated embryogenic shoots (ES), and organogenic shoots (OS). Chemometrics and cluster analysis were used to depict the correlation between the groups investigated. Metabolic profiles revealed unique metabolites in ES (serine and lactate) and in OS (2-hydroxyisobutyrate, tyrosine, histamine and homoserine). Quantitative differences as manifested by relative concentrations through heat map and fold change analyses were significant in the following comparisons: calli type, embryogenic tissues, organogenic tissues, and shoot type. In a comparison of calli types, proline, asparagine and arginine were upregulated in EC and sucrose was upregulated in OC. When comparing embryogenic tissues, monosaccharides were upregulated in EC, while proline, pyroglutamate and 4-aminobutyrate were upregulated in ES. Upon comparison of organogenic tissues, trigonelline increased by 17-fold in OS; however, monosaccharides were upregulated in OC. Finally, when comparing shoot types, 4-aminobutyrate, betaine and proline were upregulated in ES, while mono- and disaccharides were upregulated in OS. The embryogenic system was characterized by accumulation of stress related metabolites (proline); however, glycolate was identified only in the organogenesis system. The present work contributes to the understanding of the metabolic characteristics and differences between the two regeneration systems as manifested by profiles of EC, OC, and their regenerated shoots.
Key Message
Metabolic characteristics of two regeneration systems (somatic embryogenesis and organogenesis) of
Cymbopogon schoenanthus
were examined using NMR-based profiles of calli and their regenerated shoots, revealing clear qualitative and quantitative differences between the two systems at the studied developmental stages.
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