89 research outputs found
Introduction to Microsatellites: Basics, Trends and Highlights
La arveja (Pisum sativum L.) es uno de los cultivos domesticados más antiguos, altamente valorados y ampliamente cultivados en todo el mundo. Sin embargo, en Colombia esta especie carece de estudios genéticos que permitan establecer la variabilidad total. Se estudió la estructura y diversidad genética en una colección de 50 introducciones de arveja arbustiva provenientes del departamento de Nariño con 16 marcadores de repetición de secuencia simple (SSR). El promedio del contenido de información polimórfica (PIC) fue 0,62 con un total de 28 alelos y un promedio de 4 alelos por locus, siendo el locus AB71 y D21 los que amplificaron el mayor número de alelos (6). La Heterocigosidad observada (Ho) fue 0.09± 0.08 y la esperada (He) 0.42± 0.33, indicando un alto nivel de endogamia (Fis= 0.60) demostrando la naturaleza homocigota de P. sativum. Se infirieron las relaciones genéticas por medio de un análisis de similitud y un análisis Bayesiano (STRUCTURE) detectando dos agrupaciones para los genotipos de arveja analizados, con una alta similitud con las características agromorfológicas de cada genotipo. A pesar de la baja heterocigosis, los valores de heterocigosidad espera de la población total (He = 0.60) y de la agrupación 2 (He = 0.70) así como la presencia de alelos únicos y raros, muestran un nivel de variabilidad genética en la colección. Los resultados del presente estudio serán útiles para programas de pre - mejoramiento de la misma.The pea (Pisum sativum L.) is one of the oldest domesticated crops, which is highly valued and widely cultivated throughout the world. The structure and genetic diversity were studied in a collection of 50 pea shrubs accessions from department of Nariño with 16 simple sequence repeats (SSR) markers, whose average polymorphic information content (PIC) was 0.62. SSR markers amplified 28 alleles with an average of 4 alleles per locus, with locus AB71 and D21 being the ones which amplified the largest number of alleles (6). The observed heterozygosity (Ho) was 0.09 and the expected heterozygosity (He) 0.42, indicating an elevated level of inbreeding (FIS = 0.60) and demonstrating the homozygous nature of P. sativum. Genetic relationships were inferred by a similarity index (DICE) and a Bayesian Analysis (STRUCTURE), detecting two clusters for the analyzed peas’ genotypes and presenting high similarity in the agromorphological characteristics of each genotype. The combined discrimination power, using seven microsatellites molecular markers, was 99.99% indicating that these markers are very useful for genetic studies in peas. The results of this study are useful for P. Sativum pre-breeding programs.Línea de Investigación: Biotecnología VegetalSe solicito restringir el acceso hasta el 2023, debido a que se tienen varios artículos derivados en proceso de publicación
Bioinformatics: Basics, Development, and Future
Bioinformatics is an interdisciplinary scientific field of life sciences. Bioinformatics research and application include the analysis of molecular sequence and genomics data; genome annotation, gene/protein prediction, and expression profiling; molecular folding, modeling, and design; building biological networks; development of databases and data management systems; development of software and analysis tools; bioinformatics services and workflow; mining of biomedical literature and text; and bioinformatics education and training. Astronomical accumulation of genomics, proteomics, and metabolomics data as well as a need for their storage, analysis, annotation, organization, systematization, and integration into biological networks and database systems were the main driving forces for the emergence and development of bioinformatics. Current critical needs for bioinformatics among others highlighted in this chapter, however, are to understand basics and specifics of bioinformatics as well as to prepare new generation scientists and specialists with integrated, interdisciplinary, and multilingual knowledge who can use modern bioinformatics resources powered with sophisticated operating systems, software, and database/networking technologies. In this introductory chapter, I aim to give an overall picture on basics and developments of the bioinformatics field for readers with some future perspectives, highlighting chapters published in this book
Genomics Era for Plants and Crop Species – Advances Made and Needed Tasks Ahead
Historically, unintentional plant selection and subsequent crop domestication, coupled with the need and desire to get more food and feed products, have resulted in the continuous development of plant breeding and genetics efforts. The progress made toward this goal elucidated plant genome compositions and led to decoding the full DNA sequences of plant genomes controlling the entire plant life. Plant genomics aims to develop high-throughput genome-wide-scale technologies, tools, and methodologies to elucidate the basics of genetic traits/characteristics, genetic diversities, and by-product production; to understand the phenotypic development throughout plant ontogenesis with genetic by environmental interactions; to map important loci in the genome; and to accelerate crop improvement. Plant genomics research efforts have continuously increased in the past 30 years due to the availability of cost-effective, high-throughput DNA sequencing platforms that resulted in fully sequenced 100 plant genomes with broad implications for every aspect of plant biology research and application. These technological advances, however, also have generated many unexpected challenges and grand tasks ahead. In this introductory chapter, I aimed briefly to summarize some advances made in plant genomics studies in the past three decades, plant genome sequencing efforts, current state-of-the-art technological developments of genomics era, and some of current grand challenges and needed tasks ahead in the genomics and post-genomics era. I also highlighted the related book chapters contributed by different authors in this book
RNA Interference – A Hallmark of Cellular Function and Gene Manipulation
The discovery of RNA interference (RNAi) and its utilization in downregulation of specific target transcripts have revolutionized gene function analysis and elucidation of many key biochemical/genetic pathways. The insights into gene function, combined with a technology that made silencing of gene function possible using the potent, highly specific and selective RNAi approaches, provided the solution to longstanding complex obstacles in targeted crop improvementsfor agriculture, and disease therapies for medicine. In this introductory chapter, I aim briefly to cover the basics and peculiarities of RNAi and the advances made in understanding the mechanisms, components, function, evolution, application, safety and risk assessment of RNAi, while at the same time highlighting the related chapters of this book
Application of Association Mapping to Understanding the Genetic Diversity of Plant Germplasm Resources
Compared to the conventional linkage mapping, linkage disequilibrium (LD)-mapping, using the nonrandom associations of loci in haplotypes, is a powerful high-resolution mapping tool for complex quantitative traits. The recent advances in the development of unbiased association mapping approaches for plant population with their successful applications in dissecting a number of simple to complex traits in many crop species demonstrate a flourish of the approach as a “powerful gene tagging” tool for crops in the plant genomics era of 21st century. The goal of this review is to provide nonexpert readers of crop breeding community with (1) the basic concept, merits, and simple description of existing methodologies for an association mapping with the recent improvements for plant populations, and (2) the details of some of pioneer and recent studies on association mapping in various crop species to demonstrate the feasibility, success, problems, and future perspectives of the efforts in plants. This should be helpful for interested readers of international plant research community as a guideline for the basic understanding, choosing the appropriate methods, and its application
Cotton Breeding in the View of Abiotic and Biotic Stresses: Challenges and Perspectives
Global climate change manifested in average annual temperature rise and imbalance of most natural factors, such as changes in annual mean rainfall, air humidity, average temperature of cold and warm months, soil quality, etc., lead to climatic zones displacement. All these have a significant impact on agricultural production in total, including cotton growing. Cotton is one of the most important technical crops in the world. However, it is very sensitive to environmental changes. The influence of abiotic stresses (high temperature, changes in the mean rainfall and soil salinity) causes a dramatic decrease yield of this crop. Moreover, temperature anomalies and climatic zones displacement cause a change in the area of pathogens and pests distribution, which also reduces the cotton yield. One of the possible ways to increase the cotton yield under the influence of abiotic and biotic stresses is the development of new resistant varieties, using both classical breeding methods and genetic engineering achievements
Methodologies for In Vitro Cloning of Small RNAs and Application for Plant Genome(s)
The “RNA revolution” that started at the end of the 20th century with the discovery of post-transcriptional gene silencing and its mechanism via RNA interference (RNAi) placed tiny 21-24 nucleotide long noncoding RNAs (ncRNAs) in the forefront of biology as one of the most important regulatory elements in a host of physiologic processes. The discovery of new classes of ncRNAs including endogenous small interfering RNAs, microRNAs, and PIWI-interacting RNAs is a hallmark in the understanding of RNA-dependent gene regulation. New generation high-throughput sequencing technologies further accelerated the studies of this “tiny world” and provided their global characterization and validation in many biological systems with sequenced genomes. Nevertheless, for the many “yet-unsequenced” plant genomes, the discovery of small RNA world requires in vitro cloning from purified cellular RNAs. Thus, reproducible methods for in vitro small RNA cloning are of paramount importance and will remain so into the foreseeable future. In this paper, we present a description of existing small RNA cloning methods as well as next-generation sequencing methods that have accelerated this research along with a description of the application of one in vitro cloning method in an initial small RNA survey in the “still unsequenced” allotetraploid cotton genome
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