Corrigendum to "A review on urban agriculture: Technology, socio-economy, and policy" [Heliyon 8(11), (2022) Article e11583].

[This corrects the article DOI: 10.1016/j.heliyon.2022.e11583.].

A review on urban agriculture: technology, socio-economy, and policy.

It has been a challenge to support the expansion of urban agriculture (UA) in cities due to its poor economic profitability. However, it is also hard to deny the increasing benefits of UA in improving the socio-environmental dimension of cities. Hence, in this review, different aspects of UA were examined to highlight its value beyond profitability such as social, health and well-being, disaster risk reduction, and environmental perspectives. A case study and relevant policies were analyzed to determine how policy makers can bridge the gap between current and future UA practices and sustainable development. Bridging these policy gaps can help the UA sector to sustainably grow and become successfully integrated in cities. Moreover, advancements in UA technologies and plant biotechnology were presented as potential solutions in increasing the future profitability of commercial UA. Consequently, as new UA-related technologies evolve, the multidisciplinary nature of UA and its changing identity from agriculture to digital technology, similarly require adaptive policies. These policies should maximize the potential of UA in contributing to resiliency and sustainability and incentivize the organic integration of UA in cities, while equally serving social justice.

Comparative transcriptome analysis of root types in salt tolerant and sensitive rice varieties in response to salinity stress.

Salinity tolerance in rice is a very important trait, especially in areas that are affected by soil salinity, such as tsunami-devastated areas and coastal regions in rice-producing countries. The roots are the key organs that first detect and respond to salinity stress; thus, it is important to have an understanding of how roots contribute to salinity tolerance in agricultural crops. After salinity treatment of the salt tolerant (Mulai) and sensitive (IR29) rice varieties, it appeared that among the three types of roots, the L-type lateral roots (LLR) were the most sensitive to salinity stress in Mulai and the most tolerant in IR29. The nodal roots (NR) and the S-type lateral roots (SLR) were all negatively affected by salinity treatment in both rice varieties. In order to elucidate the molecular mechanism of the difference in stress response among rice root types, the RNA-seq transcriptome profiles of NR, LLR, and SLR were analyzed in Mulai and IR29. Between the two rice varieties, more transporters were found to participate in the regulation of salt tolerance in Mulai roots, such as those involved in ion and sugar transport. In IR29, many of the genes detected were associated with transcription regulation, including stress-inducible genes such as NAC, WRKY and MYB. Among the different root types, gene expression in LLR and SLR were significantly regulated in both rice varieties. Taken together, the genes identified in this study may be utilized in the varietal improvement of rice with very specific root traits that can enhance tolerance to salinity stress.

Tissue-specific expression analysis of Na+ and Cl- transporter genes associated with salt removal ability in rice leaf sheath.

BACKGROUND: A significant mechanism of salt-tolerance in rice is the ability to remove Na+ and Cl- in the leaf sheath, which limits the entry of these toxic ions into the leaf blade. The leaf sheath removes Na+ mainly in the basal parts, and Cl- mainly in the apical parts. These ions are unloaded from the xylem vessels in the peripheral part and sequestered into the fundamental parenchyma cells at the central part of the leaf sheath. RESULTS: This study aimed to identify associated Na+ and Cl- transporter genes with this salt removal ability in the leaf sheath of rice variety FL 478. From 21 known candidate Na+ and Cl- transporter rice genes, we determined the salt responsiveness of the expression of these genes in the basal and apical parts, where Na+ or Cl- ions were highly accumulated under salinity. We also compared the expression levels of these transporter genes between the peripheral and central parts of leaf sheaths. The expression of 8 Na+ transporter genes and 3 Cl- transporter genes was up-regulated in the basal and apical parts of leaf sheaths under salinity. Within these genes, OsHKT1;5 and OsSLAH1 were expressed highly in the peripheral part, indicating the involvement of these genes in Na+ and Cl- unloading from xylem vessels. OsNHX2, OsNHX3, OsNPF2.4 were expressed highly in the central part, which suggests that these genes may function in sequestration of Na+ and Cl- in fundamental parenchyma cells in the central part of leaf sheaths under salinity. Furthermore, high expression levels of 4 candidate genes under salinity were associated with the genotypic variation of salt removal ability in the leaf sheath. CONCLUSIONS: These results indicate that the salt removal ability in rice leaf sheath may be regulated by expressing various Na+ or Cl- transporter genes tissue-specifically in peripheral and central parts. Moreover, some genes were identified as candidates whose expression levels were associated with the genotypic variation of salt removal ability in the leaf sheath. These findings will enhance the understanding of the molecular mechanism of salt removal ability in rice leaf sheath, which is useful for breeding salt-tolerant rice varieties.

Bioactive bead-mediated transformation of plants with large DNA fragments.

The efficient transformation of plants with large DNA molecules containing a set of useful genes would provide vast possibilities for the genetic improvement of agricultural as well as nonagricultural plants. The development of the bioactive beads (BABs) transformation method has proven useful for introduction of large DNA molecules into plant cells. In this chapter, the BABs transformation method used for the transformation of a 100-kb BAC DNA construct containing wheat genes into rice will be presented. Furthermore, the improved production method for BABs will be described. With the conventional method for producing BABs, the bead size varies, and the larger beads tend to carry fewer DNA molecules than the smaller beads. Thus, in order to facilitate the preparation of BABs with more uniform sizes, a simple set-up -composed of a sine wave sound generator and microsyringe pump was fabricated. Using this bead-maker set-up, uniform and smaller beads could be produced which enhance the transformation efficiency.

Sequence analysis of the genome of an oil-bearing tree, Jatropha curcas L.

The whole genome of Jatropha curcas was sequenced, using a combination of the conventional Sanger method and new-generation multiplex sequencing methods. Total length of the non-redundant sequences thus obtained was 285 858 490 bp consisting of 120 586 contigs and 29 831 singlets. They accounted for ~95% of the gene-containing regions with the average G + C content was 34.3%. A total of 40 929 complete and partial structures of protein encoding genes have been deduced. Comparison with genes of other plant species indicated that 1529 (4%) of the putative protein-encoding genes are specific to the Euphorbiaceae family. A high degree of microsynteny was observed with the genome of castor bean and, to a lesser extent, with those of soybean and Arabidopsis thaliana. In parallel with genome sequencing, cDNAs derived from leaf and callus tissues were subjected to pyrosequencing, and a total of 21 225 unigene data have been generated. Polymorphism analysis using microsatellite markers developed from the genomic sequence data obtained was performed with 12 J. curcas lines collected from various parts of the world to estimate their genetic diversity. The genomic sequence and accompanying information presented here are expected to serve as valuable resources for the acceleration of fundamental and applied research with J. curcas, especially in the fields of environment-related research such as biofuel production. Further information on the genomic sequences and DNA markers is available at http://www.kazusa.or.jp/jatropha/.

The Arabidopsis SDG4 contributes to the regulation of pollen tube growth by methylation of histone H3 lysines 4 and 36 in mature pollen.

Plant SET domain proteins are known to be involved in the epigenetic control of gene expression during plant development. Here, we report that the Arabidopsis SET domain protein, SDG4, contributes to the epigenetic regulation of pollen tube growth, thus affecting fertilization. Using an SDG4-GFP fusion construct, the chromosomal localization of SDG4 was established in tobacco BY-2 cells. In Arabidopsis, sdg4 knockout showed reproductive defects. Tissue-specific expression analyses indicated that SDG4 is the major ASH1-related gene expressed in the pollen. Immunological analyses demonstrated that SDG4 was involved in the methylation of histone H3 in the inflorescence and pollen grains. The significant reduction in the amount of methylated histone H3 K4 and K36 in sdg4 pollen vegetative nuclei resulted in suppression of pollen tube growth. Our results indicate that SDG4 is capable of modulating the expression of genes that function in the growth of pollen tube by methylation of specific lysine residues of the histone H3 in the vegetative nuclei.