Molecular breeding

About: Molecular breeding is a research topic. Over the lifetime, 2120 publications have been published within this topic receiving 56908 citations.

Fish breeding method for improving CRISPR-Cas9 gene editing and passage efficiency through fish roe preserving fluid

Abstract: The invention belongs to the field of fish molecular breeding, and particularly relates to a fish breeding method for improving CRISPR-Cas9 gene editing and passage efficiency through fish roe preserving fluid. According to the method, the fish roe preserving fluid technology, the microinjection technology an the CRISPR-Cas9 gene editing technology are ingeniously combined, the targeting efficiency of the CRISPR-Cas9 gene editing technology and gene editing passage efficiency are greatly improved, the screening time needed by a gene editing method for fish breeding is obviously saved, and the method is of great significance in promoting rapid development of gene editing fish breeding.

Plant Transformation Methods and Applications

Abstract: Conventional plant breeding uses crossing, mutagenesis, and somatic hybridization for genome modification to improve crop traits by introducing new beneficial alleles from crossable species. However, because of crossing barriers and linkage drag, conventional plant breeding methods are time-consuming and require several generations of breeding and selection. To feed the several billion people living on this planet, the main aim of breeders is to increase agricultural production. Hence, new technologies need to be developed to accelerate breeding through improving genotyping and phenotyping methods. Molecular breeding technologies and their applications are discussed in some of the previous chapters. In this chapter, genetic modification technologies are introduced, including the protocols that have been used for the genetic transformation for ten major crops. Two other genetic modification methods are also introduced: (1) cisgenesis by which only beneficial alleles from crossable species are transferred into a recipient plant to enhance the use of existing gene alleles; and (2) reverse breeding to increase the available genetic diversity in breeding germplasm by blocking chromosome recombination during cell division.

Molecular Events of Rice AP2/ERF Transcription Factors

Abstract: APETALA2/ethylene response factor (AP2/ERF) is widely found in the plant kingdom and plays crucial roles in transcriptional regulation and defense response of plant growth and development. Based on the research progress related to AP2/ERF genes, this paper focuses on the classification and structural features of AP2/ERF transcription factors, reviews the roles of rice AP2/ERF genes in the regulation of growth, development and stress responses, and discusses rice breeding potential and challenges. Taken together; studies of rice AP2/ERF genes may help to elucidate and enrich the multiple molecular mechanisms of how AP2/ERF genes regulate spikelet determinacy and floral organ development, flowering time, grain size and quality, embryogenesis, root development, hormone balance, nutrient use efficiency, and biotic and abiotic response processes. This will contribute to breeding excellent rice varieties with high yield and high resistance in a green, organic manner.

Plant Breeding, Principles

Abstract: Plant breeding is a science and an art. Its essential principles are identical to those of plant evolution. With advances in knowledge, the activity has increasingly become more scientific and technical, with more predictable outcomes. The concept of genetic improvement of plants may be summarized by the mathematical expression P = G + E + GE, where P = phenotype (trait), G = genotype (genes), E = environment (in which the genes are expressed), and GE = the interaction between the genes and their environment. Consequently, if one desires to improve a trait, one may change the genotype (nature) permanently through plant breeding, or temporarily through supplementing the cultural environment (nurture). Plant breeders follow certain general steps in their work: (a) objective(s), (b) creation/assembly of variation, (c) selection, (d) evaluation, and (e) cultivar release. They also use certain methods and techniques, dictated by factors including plant mating system, source of genetic variability, and the number of genes that condition the target trait. Usually, genes for crop improvement are accessed from within biological boundaries (conventional breeding); occasionally, breeders import alien genes (molecular breeding), an approach that is intensely controversial.

Editorial: Plant Single Cell Type Systems Biology

Abstract: The molecular responses of a plant to a stress and the molecular profiles of plant organs during their development and differentiation are the reflection of the contribution from different cell types composing the plant and the organs. Hence, a major limitation to understanding plant cellular and molecular responses in different cells is the multicellular complexity of the plant or organs used to decipher them. For instance, as mentioned by Coker et al. changes in the expression levels of plant cells infected by pathogenic microbial organisms are diluted by the relative abundance of uninfected cells. This constraint has led plant biologists to select model single plant cell types such as pollen, trichomes, cotton fiber, guard cells of stomata, and various root cell types including the root hair cells, and to develop new technologies (e.g., microscopic, biochemical, and omics) to decipher their biology (Dai and Chen, 2012; Misra et al.). However, as mentioned by Schmid et al. (2015) profiling single cell types is dependent on the quantity and purity of the samples isolated as well as the use of sensitive and accurate profiling methods. The 12 articles published in this Research Topic highlight interesting methodology and biological systems applied by plant scientists to advance our knowledge in plant biology using single cell type models. Working at the level of single cell types is motivated by the need for analyzing specific biological information in the relevant cell types, which would otherwise be missed when using tissues or organs (Dai and Chen, 2012; Misra et al.). This is especially true when working on plant-microbe interactions where only a subset of cells are infected by pathogenic or mutualistic microbes. For instance, to precisely characterize the transcriptional response of Arabidopsis thaliana during infection by the oomycete Hyaloperonospora arabidopsidis (Hpa), Coker et al. applied Fluorescent Activated Cell Sorting (FACS) in separation of haustoriated and non-haustoriated Arabidopsis cells for transcriptomic analysis, allowing the discovery of 139 new Hpa-responsive genes and characterization of the local and systemic responses of the plant cells. Similarly, working on the infection of the soybean root hair cells by rhizobium, the nitrogen-fixing symbiotic soil bacterium, Hossain et al. described the integration of the transcriptomic, proteomic, phosphoproteomic, and metabolomic datasets to generate a comprehensive network of the early stage of the nodulation process. Another strategy applied by Chen et al. to gain a better understanding of the nodulation process is to compare the transcriptomes of different rhizobium-infected plant cell types. Specifically, they looked for the Medicago truncatula genes controlling infection thread formation and elongation by analyzing transcriptomic data obtained from inoculated root hair cells and the infection zone of the M. truncatula nodule. Studying plant reproduction, another complex biological process, can also benefit from single cell type analyses. Schmid et al. detailed novel methods to analyze single cell type molecular profiles such as the female gametophyte, which is composed of antipodal, central, egg, and synergid cells. Similarly, working on the male gametophyte, Lu et al. developed a pollen culture system for isolating generative cells, sperm cells and vegetative nuclei from tomato pollen grains. Plant reproduction studies can also benefit from the utility of unique single cell type models, such as Equisetum arvense, an herbaceous plant characterized by its spore reproduction. Zhao et al. analyzed the cellular and proteomic profiles of E. arvense during spore germination, revealing the high level activities of the heterotrophic and autotrophic metabolisms. The generation of unambiguous datasets from single cell types is an asset for generating systems biology models as demonstrated by Kwak et al. (2008), Sun et al. (2014) and Hossain et al. Single cell types are also considered attractive systems to precisely depict molecular phenotypes. As noted by Schiefelbein, access to single cell types now opens a new area to phenotype mutants: the establishment of molecular phenotypes (i.e., distinct molecular profiles between wild-type and mutants and their changes in response to environmental stresses). Such an approach is often limited by efficient methods to generate high quality single plant cell type samples and by the limited amount of material available for analyzing the molecular phenotype. Thus, technological development must continue to meet the needs of addressing questions at the single cell type level. Nucleic acid sequencing technologies associated with the use of performant bioinformatics tools are now enabling an accurate and sensitive quantification of single cell type transcriptomes and epigenomes. As an example, the analysis of previously published Arabidopsis root hair transcriptome data sets allowed the characterization of 5409 genes differentially expressed in root hairs versus non-root hair epidermal cells and the generation of a co-expression network (Li and Lan). Similarly, biochemical methods are quickly developing allowing access to single plant cell type proteome (Svozil et al.) and metabolome (Barkla and Vera-Estrella; Bartels and Svatos; Misra et al.). Specifically, Barkla and Vera-Estrella described the differential metabolome between specialized trichome cells from Mesembryanthemum crystallinum named epidermal bladder cells (EBC). This analysis can be expected to provide a systems level of understanding of EBC when integrated with the existing proteomic and transcriptomic data sets. Similarly, Misra et al. reviewed the most recent advances in our understanding of the guard cell metabolome. This knowledge is essential to advance our understanding of stomatal opening and closing, which have a major impact on plant transpiration, CO2 uptake and pathogen immunity. At the proteome level, Svozil et al. applied Meselect, an innovative methodology to isolate leaf epidermal, vascular and mesophyll cells. Using these samples, the authors established a proteome map of each cell type and revealed cell type specific processes. These types of studies are going to be revolutionized by the development of new imaging techniques. For instance, applying infrared-laser ablation electrospray ionization (LAESI) and UV-laser desorption/ionization (LDI) methods, less intrusive and spatially-resolved analyses of the metabolomes of single plant cell types are described in this ebook (Bartels and Svatos). These technological developments have greatly enhanced our capabilities in analyzing molecular components in different cells at an unprecedented scope and depth through omics for modeling and hypothesis generation. The integration of hypothesis generation and hypothesis testing in systems biology research will ultimately lead to a holistic view of cellular processes and molecular networks in plants and will create stepping stones toward molecular breeding and biotechnology for enhanced crop stress tolerance, yield and bioenergy.