scholarly journals Prioritization of potato genes involved in the formation of agronomically valuable traits using the SOLANUM TUBEROSUM knowledge base

2019 ◽  
Vol 23 (3) ◽  
pp. 312-319
Author(s):  
P. S. Demenkov ◽  
O. V. Saik ◽  
T. V. Ivanisenko ◽  
N. A. Kolchanov ◽  
A. V. Kochetov ◽  
...  
Keyword(s):  
Solanum Tuberosum ◽  
Knowledge Base ◽  
Candidate Genes ◽  
Genetic Relationships ◽  
Molecular Genetic ◽  
Biological Data ◽  
Targeted Mutagenesis ◽  
Pubmed Database ◽  
Genetic Mechanisms ◽  
Selection Of

The development of highly efficient technologies in genomics, transcriptomics, proteomics and metabolomics, as well as new technologies in agriculture has led to an “information explosion” in plant biology and crop production, including potato production. Only a small part of the information reaches formalized databases (for example, Uniprot, NCBI Gene, BioGRID, IntAct, etc.). One of the main sources of reliable biological data is the scientific literature. The well-known PubMed database contains more than 18 thousand abstracts of articles on potato. The effective use of knowledge presented in such a number of non-formalized documents in natural language requires the use of modern intellectual methods of analysis. However, in the literature, there is no evidence of a widespread use of intelligent methods for automatically extracting knowledge from scientific publications on cultures such as potatoes. Earlier we developed the SOLANUM TUBEROSUM knowledge base (http://www-bionet.sysbio.cytogen. ru/and/plant/). Integrated into the knowledge base information about the molecular genetic mechanisms underlying the selection of significant traits helps to accelerate the identification of candidate genes for the breeding characteristics of potatoes and the development of diagnostic markers for breeding. The article searches for new potential participants of the molecular genetic mechanisms of resistance to adverse factors in plants. Prioritizing candidate genes has shown that the PHYA, GF14, CNIH1, RCI1A, ABI5, CPK1, RGS1, NHL3, GRF8, and CYP21-4 genes are the most promising for further testing of their relationships with resistance to adverse factors. As a result of the analysis, it was shown that the molecular genetic relationships responsible for the formation of significant agricultural traits are complex and include many direct and indirect interactions. The construction of associative gene networks and their analysis using the SOLANUM TUBEROSUM knowledge base is the basis for searching for target genes for targeted mutagenesis and marker-oriented selection of potato varieties with valuable agricultural characteristics.

scholarly journals High-Throughput Genotyping of Resilient Tomato Landraces to Detect Candidate Genes Involved in the Response to High Temperatures

Genes ◽  
2020 ◽  
Vol 11 (6) ◽  
pp. 626
Author(s):  
Fabrizio Olivieri ◽  
Roberta Calafiore ◽  
Silvana Francesca ◽  
Carlo Schettini ◽  
Pasquale Chiaiese ◽  
...  
Keyword(s):  
Candidate Genes ◽  
High Temperatures ◽  
Elevated Temperatures ◽  
Genotyping By Sequencing ◽  
High Impact ◽  
Yield Trait ◽  
Genetic Mechanisms ◽  
Stable Yield ◽  
Selection Of

The selection of tolerant varieties is a powerful strategy to ensure highly stable yield under elevated temperatures. In this paper, we report the phenotypic and genotypic characterization of 10 tomato landraces to identify the best performing under high temperatures. The phenotyping of five yield-related traits allowed us to select one genotype that exhibits highly stable yield performances in different environmental conditions. Moreover, a Genotyping-by-Sequencing approach allowed us to explore the genetic variability of the tested genotypes. The high and stable yielding landrace E42 was the most polymorphic one, with ~49% and ~47% private SNPs and InDels, respectively. The effect of 26,113 mutations on proteins’ structure was investigated and it was discovered that 37 had a high impact on the structure of 34 proteins of which some are putatively involved in responses to high temperatures. Additionally, 129 polymorphic sequences aligned against tomato wild species genomes revealed the presence in the genotype E42 of several introgressed regions deriving from S. pimpinellifolium. The position on the tomato map of genes affected by moderate and high impact mutations was also compared with that of known markers/QTLs (Quantitative Trait Loci) associated with reproductive and yield-related traits. The candidate genes/QTLs regulating heat tolerance in the selected landrace E42 could be further investigated to better understand the genetic mechanisms controlling traits for high and stable yield trait under high temperatures.

scholarly journals High-throughput sequencing techniques to flax genetics and breeding

2020 ◽  
Author(s):  
Alena Olegovna Akhmetshina ◽  
Ksenia Vladimirovna Strygina ◽  
Elena Konstantinovna Khlestkina ◽  
Elisaveta Alexandrovna Porokhovinova ◽  
Nina Borisovna Brutch
Keyword(s):  
Stress Responses ◽  
High Throughput Sequencing ◽  
Molecular Genetic ◽  
Stress Factors ◽  
Fundamental Interest ◽  
Genetic Mechanisms ◽  
High Marker Density ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing ◽  
Selection Of

Flax (Lnum usitatssimum L.) is an important oil and fiber crop. Using modern methods for flax breeding allows accelerating the introduction of some desired genes into the genotypes of future varieties. Today, an important condition for their creation is the development of research, that is based on next-generation sequencing (NGS). This review summarizes the results obtained using NGS sequencing in flax research. To date, a linkage map with a high marker density has been obtained for L. usitatssimum, which is already being used for a more efficient search for quantitative traits loci. Comparative studies of transcriptomes and miRNomes of flax under stress and in control conditions elucidated molecular-genetic mechanisms of abiotic and biotic stress responses. The very accurate model for genomic selection of flax resistant to pasmo was constructed. Based on NGS-sequencing also some details of the genus Linum evolution were clarified. The knowledge systematized in the review can be useful for researchers working in flax breeding and whereas fundamental interest for understanding the phylogenetic relationships within the genus Linum, the ontogenesis, and the mechanisms of the response of flax plants to various stress factors.

Genetics of Pediatric Irritability

2019 ◽  
pp. 149-170
Author(s):  
Meridith L. Eastman ◽  
Ashlee A. Moore ◽  
Roxann Roberson-Nay
Keyword(s):  
Environmental Factors ◽  
Candidate Genes ◽  
Association Studies ◽  
Molecular Genetic ◽  
Human Studies ◽  
Genome Wide Association Studies ◽  
Genetic Studies ◽  
Genome Wide ◽  
Literature Searches ◽  
Selection Of

This chapter provides an overview of behavioral and molecular genetics of pediatric irritability. Literature searches using PubMed and PsycInfo databases yielded 37 relevant animal and human studies on irritability. Studies of rodent and primate models initially suggested a genetic etiology for the trait and influenced selection of candidate genes for study in human studies. Behavioral genetic studies of irritability suggest that pediatric irritability is likely influenced by additive genetic and nonshared unique environmental factors, with little to no influence of dominant genetic or shared family environmental factors. Molecular genetic studies have been largely limited to candidate genes with a few emerging genome-wide association studies (GWAS). Results from the candidate gene literature on irritability are inconclusive, and GWAS in clinical populations has yielded limited findings. Future genetic studies of irritability would benefit from the use of appropriate phenotypic measures, adequate sample sizes, and multimethod and longitudinal approaches.

scholarly journals Genome-wide studies of knee osteoarthritis (review)

2021 ◽  
Author(s):  
Vitaly B. Novakov ◽  
Olga N. Novakova ◽  
Mikhail I. Churnosov
Keyword(s):  
Knee Osteoarthritis ◽  
Candidate Genes ◽  
Molecular Genetic ◽  
Keywords Knee ◽  
Significance Level ◽  
Polymorphic Loci ◽  
Knee Oa ◽  
Genome Wide ◽  
Genetic Mechanisms ◽  
And Control

Introduction. Knee Osteoarthritis (OA) is a multifactorial disease resulting from the interaction of many environmental, epigenetic and genetic risk factors, and the latter account for 40% to 65%. Genetic bases of the knee OA based on genome-wide association search (GWAS) are being actively studied by many scientific teams around the world. At the same time, the results obtained are often contradictory and ambiguous, as for the conducted replicative studies of knee OA. This dictates the need for additional replicative studies in various populations, including populations of Russia, which are characterized by significant ethno-territorial variability, in order to identify specific GWAS-significant polymorphic markers of candidate genes associated with OA in these individual populations. The aim of the study was to analyze genome-wide studies of knee OA and to establish GWAS-significant polymorphic loci associated with OA. Materials and methods. The search for publications was carried out in the electronic databases PubMed, PubMedCentral, eLIBRARY, in the GWAS catalog for the period from 2008 to the present by the keywords: knee osteoarthritis, GWAS studies, candidate genes. Results. First, to date, 14 genome-wide studies of knee OA have been performed, as a result of which about 80 GWAS-significant polymorphic loci associated with the risk of knee OA have been identified. Secondly, all GWAS of the knee OA were carried out abroad on samples from various foreign populations, and the samples from the Russian Federation were not included in these studies. Third, only two GWAS-significant polymorphic loci for OA (rs143384 of the GDF5 gene and rs3771501 of the TGFA gene) were replicated at the genome-wide significance level (p5x10-08) in two different studies. Fourth, the data obtained indicate the presence of two regions of chromosomes (6p21.32 and 7q22.3), in which the largest number of GWAS-significant polymorphic loci for OA is located - 3SNPs in each (6p21.32 - rs10947262, rs7775228, rs9277552; 7q22.3 - rs4730250, rs10953541, rs3815148). Fifth, with an increase in the volume of the studied samples of patients and control in genome-wide studies of knee OA, the number of identified GWAS-significant polymorphisms also increases. Conclusion. The main genome-wide studies of knee OA were reviewed and GWAS-significant polymorphisms associated with OA were identified. The obtained materials on GWAS-significant loci can be used both in the selection of polymorphisms in replicative studies of OA in various populations of Russia, and for expanding the understanding of the molecular genetic mechanisms of the disease development.

scholarly journals THE SOLANUM TUBEROSUM KNOWLEDGE BASE: THE SECTION ON MOLECULAR-GENETIC REGULATION OF METABOLIC PATHWAYS

2018 ◽  
Vol 22 (1) ◽  
pp. 8-17 ◽  
Author(s):  
T. V. Ivanisenko ◽  
O. V. Saik ◽  
P. S. Demenkov ◽  
V. K. Khlestkin ◽  
E. K. Khlestkina ◽  
...  
Keyword(s):  
Solanum Tuberosum ◽  
Knowledge Base ◽  
Metabolic Pathways ◽  
Molecular Genetic ◽  
Genetic Regulation

Practical R for biologists: an introduction

2021 ◽  
Keyword(s):  
Statistical Tests ◽  
Statistical Modelling ◽  
Biological Data ◽  
Early Years ◽  
Main Text ◽  
Biological Data Analysis ◽  
Base Functions ◽  
Almost All ◽  
Selection Of ◽  
R Functions

Abstract R is an open-source statistical environment modelled after the previously widely used commercial programs S and S-Plus, but in addition to powerful statistical analysis tools, it also provides powerful graphics outputs. In addition to its statistical and graphical capabilities, R is a programming language suitable for medium-sized projects. This book presents a set of studies that collectively represent almost all the R operations that beginners, analysing their own data up to perhaps the early years of doing a PhD, need. Although the chapters are organized around topics such as graphing, classical statistical tests, statistical modelling, mapping and text parsing, examples have been chosen based largely on real scientific studies at the appropriate level and within each the use of more R functions is nearly always covered than are simply necessary just to get a p-value or a graph. R comes with around a thousand base functions which are automatically installed when R is downloaded. This book covers the use of those of most relevance to biological data analysis, modelling and graphics. Throughout each chapter, the functions introduced and used in that chapter are summarized in Tool Boxes. The book also shows the user how to adapt and write their own code and functions. A selection of base functions relevant to graphics that are not necessarily covered in the main text are described in Appendix 1, and additional housekeeping functions in Appendix 2.

scholarly journals The Population Structure and Selection Signal Analysis of Shenxian Pigs Based on Genome Resequencing Technology

2021 ◽  
Author(s):  
Diao Liu ◽  
Chunlian Lu ◽  
Shang Li ◽  
Mengyu Jia ◽  
Yutao Miao ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Meat Quality ◽  
Genetic Relationships ◽  
Animal Husbandry ◽  
Hebei Province ◽  
Whole Genome ◽  
Genome Resequencing ◽  
Large White ◽  
Bioinformatics Analyses ◽  
Pig Breeds

Abstract Shenxian pigs are the only local black pig of Hebei Province, and were listed in the Genetics of Livestock and Poultry Resources of China in 2016. This breed of pig is considered to be a valuable local pig germplasm genetic resource in China. When compared with other introduced pig breeds, the Shenxian pig breed is characterized with early sexual maturity, short oestrus intervals, large litter sizes, and good meat quality, which are all of good research significance. However, the Shenxian pig variety was previously declared extinct in 2004 due to the introduction of a large number of foreign pig breeds. In order to preserve and study the Shenxian pig breed, the Hebei Zhengnong Animal Husbandry Co., Ltd. was established in Hebei Province for the purpose of preserving the purified Shenxian pig strain. In the present study, in order to understand the genetic variations of Shenxian pigs, identify selected regions related to superior traits, and accelerate the breeding processes of Shenxian pigs, the whole genome of the Shenxian pigs was resequenced and compared with that of large white pigs. The goal was to explore the germplasm characteristics of Shenxian pigs.The results obtained in this research investigation revealed that the genetic relationships of the Shenxian pig breed were complex, and that sub-populations could be identified within the general population. A total of 23M SNP sites were obtained by whole genome resequencing, and 1,509 selected sites were obtained via bioinformatics analyses. It was determined after annotation that a total of 19 genes were enriched in three items of bioengineering, molecular function, and cell composition.During this research investigation, the aforementioned 19 genes were subjected to GO and KEGG analyses. Subsequently, the candidate genes related to cell proliferation were obtained (DMTF1 and WDR5), which were considered to possibly be related to the slow growth and development of Shenxian pigs. In addition, the candidate genes related to lactation were obtained (CSN2 and CSN3). However, no genes related to meat quality traits were successfully screened.

scholarly journals Development of KASP Markers for Germplasm Characterization and Fingerprinting Identification of Broccoli in China

2020 ◽  
Author(s):  
Yusen Shen ◽  
Jiansheng Wang ◽  
Huifang Yu ◽  
Xiaoguang Sheng ◽  
Zhenqing Zhao ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Marker Assisted Selection ◽  
Genetic Relationships ◽  
Cost Effective ◽  
Germplasm Characterization ◽  
2D Barcode ◽  
New Type ◽  
Generation Sequencing ◽  
Kasp Markers ◽  
Selection Of

Abstract Background: Broccoli (Brassica oleracea var. italica) is a vegetable widely cultivated in China. Many new-type broccoli cultivars were bred and developed by Chinese breeders during the recent three decades. However, the broccoli cultivar nomenclature and detailed information of genetic relationships among broccoli germplasms are unclear. Results: The present study identified millions of SNPs by next-generation sequencing of 23 representative broccoli lines. Through several steps of selection, 100 SNPs were successfully converted into KASP markers, and used to evaluate the genetic diversity, genetic relationship, and population structure of 392 broccoli accessions, which represent the mainly broccoli breeding materials in China. The initial, introduced and improved accessions were well clustered, though some accessions were overlapped between groups, probably reflecting the fact that breeding activities led to genetic similarities. To make the KASP genotyping more efficient and cost-effective, 25 of the 100 KASPs were selected for fingerprinting of all accessions, and the 2D barcode contained fingerprinting information were generated for elite varieties. Conclusion: The KASP markers developed in this study provided an efficient way for germplasm characterization, DNA fingerprinting, seed purity identification, and marker-assisted selection of broccoli in China.

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