Genomics Researches and Their Applications in Plant Breeding at PAG XXIV Conference

( Franz Marielle Nogoy ),( Shadi Rahimi ),( Kwon-kyoo Kang ),( Yong-gu Cho ) 한국육종학회 2016 Plant Breeding and Biotechnology Vol.4 No.1

The rise of whole genome sequences of different plants provided more understanding about the gene regulation and genome evolution in further studying plants. More and more pathways and networks are identified by novel gene discoveries. Therefore, the Plant and Animal Genome Conference (PAG XXIV) provides a good venue to share the recent progress in the area of plant research genome sequencing technologies in various plants. However, this information can make a powerful system for developing improved crop varieties. By the way, the genome annotation and assembly is an essential key for breeding of stress-tolerant plants. PAG XXIV demonstrated different works about the extensive use of genomic databases accompanied by bioinformatics tools to accelerate breeding methods, discovery of new approaches to genomics, further increasing biomass of bioenergy crops, and explaining the genetic mechanisms in plant growth and defense. This review article summarizes some of the researches in various plants of rice, corn, wheat, cottonwood, switchgrasses, Thinopyrum, wheatgrass and Arabidopsis presented in PAG XXIV with the focus on genome technologies and their applications in plant breeding.

Comparative genomics of 151 plant-associated bacteria reveal putative mechanisms underlying specific interactions between bacteria and plant hosts

Hongsheng Cai,Yan Bai,Changhong Guo 한국유전학회 2018 Genes & Genomics Vol.40 No.8

Although much work has explored how microbes can benefit plant growth, the mechanisms underlying this intriguing process remain largely unknown, especially considering the diversity of bacteria that surrounds plants. The objective of the present study was to identify bacterial genes contributing to plant–microbe associations, beneficial effects, and host specificities. For this purpose, comparative genomics investigation of 151 plant-associated bacteria was performed. A principal component analysis of seven key genomic features revealed patterns in the specific properties of these bacteria: N2- fixing bacteria were more closely related to pathogenic ones than to beneficial bacteria. A common set of genes over-represented in these plant-associated bacteria were found to be remarkably similar in terms of (1) genetic information processing, (2) amino acid metabolism, (3) metabolism of cofactors and vitamins, (4) nucleotide metabolism, (5) human diseases, and (6) metabolism of terpenoids and polyketides. Although we did not detect a common genetic basis for these beneficial effects, further in-depth analysis revealed that each of five beneficial bacterial groups shared specific gene sets. Functional annotation showed that environmental information processing, genetic information processing and cellular processes predominated in these beneficial groups. Hypothesizing that plant-associated bacteria may have overlapping strategies to colonize their plant hosts, we successfully identified many putative genes that determine host specificities. Most of these genes were classified as transcription factors, enzymes, transporters, and chemotaxis regulators. Comparative genomics provides a powerful tool for helping to identify genes that are common among species. Genome-based views of plant-associated bacteria reveal specific interactions between bacteria and plant hosts.

Complete genome sequencing and analysis of endophytic <i>Sphingomonas</i> sp. LK11 and its potential in plant growth

Asaf, Sajjad,Khan, Abdul Latif,Khan, Muhammad Aaqil,Al-Harrasi, Ahmed,Lee, In-Jung Springer International Publishing 2018 3 Biotech Vol.8 No.9

<P>Our study aimed to elucidate the plant growth-promoting characteristics and the structure and composition of <I>Sphingomonas</I> sp. LK11 genome using the single molecule real-time (SMRT) sequencing technology of Pacific Biosciences. The results revealed that LK11 produces different types of gibberellins (GAs) in pure culture and significantly improves soybean plant growth by influencing endogenous GAs compared with non-inoculated control plants. Detailed genomic analyses revealed that the <I>Sphingomonas</I> sp. LK11 genome consists of a circular chromosome (3.78 Mbp; 66.2% G+C content) and two circular plasmids (122,975 bps and 34,160 bps; 63 and 65% G+C content, respectively). Annotation showed that the LK11 genome consists of 3656 protein-coding genes, 59 tRNAs, and 4 complete rRNA operons. Functional analyses predicted that LK11 encodes genes for phosphate solubilization and nitrate/nitrite ammonification, which are beneficial for promoting plant growth. Genes for production of catalases, superoxide dismutase, and peroxidases that confer resistance to oxidative stress in plants were also identified in LK11. Moreover, genes for trehalose and glycine betaine biosynthesis were also found in LK11 genome. Similarly, <I>Sphingomonas</I> spp. analysis revealed an open pan-genome and a total of 8507 genes were identified in the <I>Sphingomonas</I> spp. pan-genome and about 1356 orthologous genes were found to comprise the core genome. However, the number of genomes analyzed was not enough to describe complete gene sets. Our findings indicated that the genetic makeup of <I>Sphingomonas</I> sp. LK11 can be utilized as an eco-friendly bioresource for cleaning contaminated sites and promoting growth of plants confronted with environmental perturbations.</P><P><B>Electronic supplementary material</B></P><P>The online version of this article (10.1007/s13205-018-1403-z) contains supplementary material, which is available to authorized users.</P>

Genome editing in potato plants by agrobacterium-mediated transient expression of transcription activator-like effector nucleases

Jin Ma,Heng Xiang,Danielle J. Donnelly,Fan-Rui Meng,Huimin Xu,Dion Durnford,Xiu-Qing Li 한국식물생명공학회 2017 Plant biotechnology reports Vol.11 No.5

Genome editing (also known as targeted mutation) has promise for molecular breeding. Compared with the CRISPR/Cas9 system, the transcription activator-like effector nucleases (TALENs) have likely a lesser off-target rate in genome editing. Both a rapid test system for the functionality of designed TALENs and an effective delivery system for introducing the TALENs to plants are critical for successful target mutation. TALENs have usually been tested in protoplasts or introduced to plants with viral vectors. However, plant regeneration from protoplast culture can generate extensive somatic variation. Viral vectors are not always available, and plants edited by these vectors usually require virus elimination. Here, we used a nonviral, Agrobacterium-mediated transient expression approach, to serve both rapid test and effective delivery of TALENs into two vegetatively propagated potato cultivars, Solanum tuberosum Russet Burbank and Shepody. Two TALENs with different molecular weights (22 and 27 aarepeat modules) were expressed to target two endogenous genes (starch branching enzyme and an acid invertase) by Agrobacterium-mediated infiltration (agroinfiltration) into leaves of potato plants. The infiltrated leaf DNA was analyzed using restriction site loss assay and subsequent DNA sequencing. Deep sequencing of these tetraploid cultivars was also conducted to determine the zygosity at the targeted chromosomal loci. TALENs, with different molecular weights, successfully agroinfiltrated and induced mutations at both targeted loci.

Functional studies of transcription factors involved in plant defenses in the genomics era

Seo, Eunyoung,Choi, Doil,Choi Oxford University Press 2015 Briefings in functional genomics Vol.14 No.4

<P>Plant transcription factors (TFs) play roles in diverse biological processes including defense responses to pathogens. Here, we provide an overview of recent studies of plant TFs with regard to defense responses. TFs play roles in plant innate immunity by regulating genes related to pathogen-associated molecular pattern-triggered immunity, effector-triggered immunity, hormone signaling pathways and phytoalexin synthesis. Currently, genome-wide phylogenetic and transcriptomic analyses are as important as functional analyses in the study of plant TFs. The integration of genomics information with the knowledge obtained from functional studies provides new insights into the regulation of plant defense mechanisms as well as engineering crops with improved resistance to invading pathogens.</P>

An online database for genome information of agricultural plants

Kim, ChangKug,Park, DongSuk,Seol, YoungJoo,Yoon, UngHan,Lee, GangSeob,Hahn, JangHo Biomedical Informatics 2012 Bioinformation Vol.8 No.21

<P>The integration-based genome database provides useful information through a user-friendly web interface that allows analysis of comparative genome for agricultural plants. We have concentrated on the functional bioinformatics of major agricultural resources, such as rice, Chinese cabbage, rice mutant lines, and microorganisms. The major functions are focused on functional genome analysis, including genome projects, gene expression analysis, gene markers with genetic map, analysis tools for comparative genome structure, and genome annotation in agricultural plants.</P><P><B>Availability</B></P><P>The database is available for free at http://nabic.naas.go.kr/</P>

BIOTECHNOLOGY START-UPS AND THE GENETIC ENGINEERING OF PLANTS

Matteo Cagnasso 중앙대학교 법학연구원 문화.미디어.엔터테인먼트법연구소 2023 문화.미디어.엔터테인먼트 법 Vol.17 No.1

Scientific and technological progress in agricultural and plant biotechnology shifted from genetic transformation, the basis of GMO products, to genome editing, leading to next-generation agronomic products. While plant genetic transformation is focused on bringing an exogenous gene to be expressed in plant genomes, genome editing is based on modifying the sequence of endogenous genes. Genome editing is, therefore, seen as a more accessible and cheaper technique, as the genes to be modified are already present in the genome of the target species. At the same time, genetic transformation requires the creation of a transgene and a technique to insert it into the genome. Genome editing has shown to be an ideal technique for innovative start-ups. While GMOs obtained from plant transformation must be authorized to be exploited in a market, according to many legal systems, as they are seen as a potential threat to human and animal health or the environment, there is no unanimous position regarding genome-edited plants. So legal systems worldwide have adopted very different positions on their regulation. The article discusses the scientific and legal factors that constitute why this technological innovation has led to the special favoring of innovative start-ups in the biotechnology field.

Detection of mPing mobilization in transgenic rice plants

박두리,최익영,김남수 한국유전학회 2020 Genes & Genomics Vol.42 No.1

Background Various kinds of transposable elements (TEs) constitute high proportions of eukaryotic genomes. Although most of these TEs are not actively mobile, genome stress can induce mobilization of dormant TEs. Transgenic plants undergo tissue culture and subsequent whole-plant regeneration, which can cause genomic stress and in turn induce mobilization of inactive TEs. Objectives To investigate the activation of transposable elements on the genome wide of the GM plant. Methods Transposon activities were analyzed in three transgenic rice plants carrying the insect resistance gene Cry1Ac and an herbicide resistance gene by the transposon display technique. These three transgenic plants were derived from a leading Korean rice variety, Illmi. Results We detected seven mobile activities in the mPing element, which is a MITE family transposon. The identity of the novel fragments in the gel display was confirmed by checking TAA target site duplication via sequence analysis. The genomic integration sites were all on different chromosomes, and the integrations were specific to either one or two T1 transgenic lines, except for one common integration on chromosome 4. One integration was in the 5′-UTR of the Glycerol3-phosphate acyltransferase 8 gene, two integrations were in introns of expressed genes, and the other four integrations were in intergenic regions. Conclusion Thus, novel mobilization of dormant TEs occurs in transgenic plants, which must be considered in the generation of genetically modified crops (GM crops).

Exploring the role and characterization of Burkholderia cepacia CD2: a promising eco-friendly microbial fertilizer isolated from long-term chemical fertilizer-free soil

HyunWoo Son,Justina Klingaite,Sihyun Park,Jae-Ho Shin 한국응용생명화학회 2023 Journal of Applied Biological Chemistry (J. Appl. Vol.66 No.-

In the pursuit of sustainable and environmentallyfriendly agricultural practices, we conducted an extensive study on the rhizosphere bacteria inhabiting soils that have been devoid of chemical fertilizers for an extended period exceeding 40 years. Through this investigation, we isolated a total of 80 species of plant growth-promoting rhizosphere bacteria and assessed their potential to enhance plant growth. Among these isolates, Burkholderia cepacia CD2 displayed remarkable plant growth-promoting activity, making it an optimal candidate for further analysis. Burkholderia cepacia CD2 exhibited a range of beneficial characteristics conducive to plant growth, including phosphate solubilization, siderophore production, denitrification, nitrate utilization, and urease activity. These attributes are well-known to positively influence the growth and development of plants. To validate the taxonomic classification of the strain, 16S rRNA gene sequencing confirmed its placement within the Burkholderia genus, providing further insights into its phylogenetic relationship. To delve deeper into the potential mechanisms underlying its plant growthpromoting properties, we sought to confirm the presence of specific genes associated with plant growth promotion in CD2. To achieve this, whole genome sequencing (WGS) was performed by Plasmidsaurus Inc. (USA) utilizing Oxford Nanopore technology (Abingdon, UK). The WGS analysis of the genome of CD2 revealed the existence of a subsystem function, which is thought to be a pivotal factor contributing to improved plant growth. Based on these findings, it can be concluded that Burkholderia cepacia CD2 has the potential to serve as a microbial fertilizer, offering a sustainable alternative to chemical fertilizers.

The Pragmatic Introduction and Expression of Microbial Transgenes in Plants

( Sajid Ali ),( Soon-ki Park ),( Won-chan Kim ) 한국미생물 · 생명공학회 2018 Journal of microbiology and biotechnology Vol.28 No.12

Several genetic strategies have been proposed for the successful transformation and expression of microbial transgenes in model and crop plants. Here, we bring into focus the prominent applications of microbial transgenes in plants for the development of disease resistance; mitigation of stress conditions; augmentation of food quality; and use of plants as “bioreactors” for the production of recombinant proteins, industrially important enzymes, vaccines, antimicrobial compounds, and other valuable secondary metabolites. We discuss the applicable and cost-effective approaches of transgenesis in different plants, as well as the limitations thereof. We subsequently present the contemporary developments in targeted genome editing systems that have facilitated the process of genetic modification and manifested stable and consumer-friendly, genetically modified plants and their products. Finally, this article presents the different approaches and demonstrates the introduction and expression of microbial transgenes for the improvement of plant resistance to pathogens and abiotic stress conditions and the production of valuable compounds, together with the promising research progress in targeted genome editing technology. We include a special discussion on the highly efficient CRISPR-Cas system helpful in microbial transgene editing in plants.