CRISPR-Cas9/Cpf1 system with its unique gene targeting efficiency, could be an important tool for functional study of early developmental genes through the generation of successful knockout plants. The introduction and utilization of systems biology approaches have identified several genes that are involved in early development of a plant and with such knowledge a robust tool is required for the functional validation of putative candidate genes thus obtained. The development of the CRISPR-Cas9/Cpf1 genome editing system has provided a convenient tool for creating loss of function mutants for genes of interest. The present study utilized CRISPR/Cas9 and CRISPR-Cpf1 technology to knock out an early developmental gene EPFL9 (Epidermal Patterning Factor like-9, a positive regulator of stomatal development in Arabidopsis) orthologue in rice. Germ-line mutants that were generated showed edits that were carried forward into the T2 generation when Cas9-free homozygous mutants were obtained. The homozygous mutant plants showed more than an eightfold reduction in stomatal density on the abaxial leaf surface of the edited rice plants. Potential off-target analysis showed no significant off-target effects. This study also utilized the CRISPR-LbCpf1 (Lachnospiracae bacterium Cpf1) to target the same OsEPFL9 gene to test the activity of this class-2 CRISPR system in rice and found that Cpf1 is also capable of genome editing and edits get transmitted through generations with similar phenotypic changes seen with CRISPR-Cas9. This study demonstrates the application of CRISPR-Cas9/Cpf1 to precisely target genomic locations and develop transgene-free homozygous heritable gene edits and confirms that the loss of function analysis of the candidate genes emerging from different systems biology based approaches, could be performed, and therefore, this system adds value in the validation of gene function studies.

The aim of this work was to identify which aspects of photosynthetic metabolism respond most sensitively to leaf water deficit. Spinach (Spinacia oleracea L.) leaf discs were floated on sorbitol concentrations of increasing molarity and changes of the protoplast volume were estimated using [(14)C]sorbitol and (3)H2O penetration. Detached leaves were also wilted until 10% of their fresh weight was lost. Photosynthesis was studied at very high external CO2 concentrations, to eliminate the effect of closing stomata. There was no large inhibition of CO2 fixation after wilting leaves, or until the external water deficit was greater than-1.2 MPa. However, partitioning changed markedly at these moderate water deficits: more sucrose and less starch was made. When an inhibition of CO2-saturated photosynthesis did appear at a water deficit of-2.0 MPa and above, measurements of chlorophyll-fluorescence quenching and metabolite levels showed the thylakoid reactions were not especially susceptible to short-term water stress. The inhibition was accompanied by a small increase of the triose phosphate: ribulose-1,5-bisphosphate ratio, showing regeneration of ribulose-1,5-bisphosphate was affected. However, there was also a general increase of the estimated concentrations of most metabolites, indicating that there is no specific site for the inhibition of photosynthesis. Increasing water deficit led to a large increase of fructose-2,6-bisphosphate. This is explained in terms of a simultaneous increase of fructose-6-phosphate and inorganic phosphate as the cell shrinks. The high fructose-2,6-bisphosphate led to the accumulation of triose phosphates, and the potential significance of this for protection against photoinhibition is discussed. There was an increase in the extractable activity of sucrose-phosphate synthase. This was only detected when the enzyme was assayed in conditions which distinguish between different kinetic forms which have previously been identified in spinach leaves. It is proposed that activation of sucrose-phosphate synthase is one of the first sites at which spinach leaves respond to a rising water deficit. This could be of importance for osmoregulation.

A tomato line (IL9-2-5) of the cultivated species, Lycopersicon esculentum, carrying a 9 cM introgression from the wild species, Lycopersicon pennelli, produces fruit with high soluble solids content (Brix), an important determinant of fruit quality for processing. Two quantitative trait loci (QTLs) relating to fruit soluble solids content have been identified within the introgressed segment. One of these QTLs (PW-9-2-5) is silent under the growth conditions used in this study, while a second (Brix-9-2-5) has been shown to encode a fruit apoplastic invertase (Lin5) with altered kinetic properties. In this study, we have undertaken a detailed biochemical analysis of the introgression line to attempt to gain an understanding of the metabolic changes associated with increased fruit soluble solids. Increased Brix in ripe fruit was shown to be the result of increased sucrose and glucose, with a more minor contribution from aspartate and alanine. The introgression leads to a pronounced increase in apoplastic invertase activity in the columella tissue that extends throughout fruit development. Furthermore, columella tissue from IL9-2-5 fruit has a greater capacity to take up exogenously supplied sucrose, an observation that is consistent with the kinetic properties of the introgressed Lin5 allele. Apart from the increase in mature fruit sugar and increases in some amino acids, metabolite profiling revealed few other metabolic perturbations in fruit from IL9-2-5. The only other major change was a dramatic increase in starch accumulation at earlier stages of fruit metabolism. This occurred without any increase in the activity of the enzymes of sucrose metabolism or starch synthesis and may therefore be driven by increased availability of sucrose. We conclude that the major factor that leads to increased fruit sugar in IL9-2-5 is an increase in the capacity to take up sucrose unloaded from the phloem.

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