Development of resources and tools for mapping genetic sources of phenotypic variation

USDA-ARS?s Scientific Manuscript database

Commercial and experimental genetic resources were established and investigated for a range of reproductive and disease susceptibility phenotypes. The phenotyping efforts were accompanied with RNA and whole genome sequencing and novel assemblies of the swine genome. The efforts were complemented wit...

Genetic conservation in applied tree breeding programs.

Treesearch

R. Johnson; B. St. Clair; S. Lipow

2001-01-01

This paper reviews how population size and structure impacts the maintenance of genetic variation in breeding and gene resource populations. We discuss appropriate population sizes for low frequency alleles and point out some examples of low frequency alleles in the literature. Development of appropriate breeding populations and gene resource populations are discussed...

Flexible Job-Shop Scheduling with Dual-Resource Constraints to Minimize Tardiness Using Genetic Algorithm

NASA Astrophysics Data System (ADS)

Paksi, A. B. N.; Ma'ruf, A.

2016-02-01

In general, both machines and human resources are needed for processing a job on production floor. However, most classical scheduling problems have ignored the possible constraint caused by availability of workers and have considered only machines as a limited resource. In addition, along with production technology development, routing flexibility appears as a consequence of high product variety and medium demand for each product. Routing flexibility is caused by capability of machines that offers more than one machining process. This paper presents a method to address scheduling problem constrained by both machines and workers, considering routing flexibility. Scheduling in a Dual-Resource Constrained shop is categorized as NP-hard problem that needs long computational time. Meta-heuristic approach, based on Genetic Algorithm, is used due to its practical implementation in industry. Developed Genetic Algorithm uses indirect chromosome representative and procedure to transform chromosome into Gantt chart. Genetic operators, namely selection, elitism, crossover, and mutation are developed to search the best fitness value until steady state condition is achieved. A case study in a manufacturing SME is used to minimize tardiness as objective function. The algorithm has shown 25.6% reduction of tardiness, equal to 43.5 hours.

Genetics Home Reference: Woodhouse-Sakati syndrome

MedlinePlus

... low amounts of hormones that direct sexual development (hypogonadism), which typically becomes apparent during adolescence. Without hormone ... Resources Genetic Testing (1 link) Genetic Testing Registry: Hypogonadism, diabetes mellitus, alopecia, mental retardation and electrocardiographic abnormalities ...

Poultry genetic resource conservation using primordial germ cells

PubMed Central

NAKAMURA, Yoshiaki

2016-01-01

The majority of poultry genetic resources are maintained in situ in living populations. However, in situ conservation of poultry genetic resources always carries the risk of loss owing to pathogen outbreaks, genetic problems, breeding cessation, or natural disasters. Cryobanking of germplasm in birds has been limited to the use of semen, preventing conservation of the W chromosome and mitochondrial DNA. A further challenge is posed by the structure of avian eggs, which restricts the cryopreservation of ova and fertilized embryos, a technique widely used for mammalian species. By using a unique biological property and accessibility of avian primordial germ cells (PGCs), precursor cells for gametes, which temporally circulate in the vasculature during early development, an avian PGC transplantation technique has been established. To date, several techniques for PGC manipulation including purification, cryopreservation, depletion, and long-term culture have been developed in chickens. PGC transplantation combined with recent advanced PGC manipulation techniques have enabled ex situ conservation of poultry genetic resources in their complete form. Here, the updated technologies for avian PGC manipulation are introduced, and then the concept of a poultry PGC-bank is proposed by considering the biological properties of avian PGCs. PMID:27210834

Genetics of behavior in the silver fox.

PubMed

Kukekova, Anna V; Temnykh, Svetlana V; Johnson, Jennifer L; Trut, Lyudmila N; Acland, Gregory M

2012-02-01

The silver fox provides a rich resource for investigating the genetics of behavior, with strains developed by intensely selective breeding that display markedly different behavioral phenotypes. Until recently, however, the tools for conducting molecular genetic investigations in this species were very limited. In this review, the history of development of this resource and the tools to exploit it are described. Although the focus is on the genetics of domestication in the silver fox, there is a broader context. In particular, one expectation of the silver fox research is that it will be synergistic with studies in other species, including humans, to yield a more comprehensive understanding of the molecular mechanisms and evolution of a wider range of social cognitive behaviors.

Genomic resources in fruit plants: an assessment of current status.

PubMed

Rai, Manoj K; Shekhawat, N S

2015-01-01

The availability of many genomic resources such as genome sequences, functional genomics resources including microarrays and RNA-seq, sufficient numbers of molecular markers, express sequence tags (ESTs) and high-density genetic maps is causing a rapid acceleration of genetics and genomic research of many fruit plants. This is leading to an increase in our knowledge of the genes that are linked to many horticultural and agronomically important traits. Recently, some progress has also been made on the identification and functional analysis of miRNAs in some fruit plants. This is one of the most active research fields in plant sciences. The last decade has witnessed development of genomic resources in many fruit plants such as apple, banana, citrus, grapes, papaya, pears, strawberry etc.; however, many of them are still not being exploited. Furthermore, owing to lack of resources, infrastructure and research facilities in many lesser-developed countries, development of genomic resources in many underutilized or less-studied fruit crops, which grow in these countries, is limited. Thus, research emphasis should be given to those fruit crops for which genomic resources are relatively scarce. The development of genomic databases of these less-studied fruit crops will enable biotechnologists to identify target genes that underlie key horticultural and agronomical traits. This review presents an overview of the current status of the development of genomic resources in fruit plants with the main emphasis being on genome sequencing, EST resources, functional genomics resources including microarray and RNA-seq, identification of quantitative trait loci and construction of genetic maps as well as efforts made on the identification and functional analysis of miRNAs in fruit plants.

Genetic selection and conservation of genetic diversity*.

PubMed

Blackburn, H D

2012-08-01

For 100s of years, livestock producers have employed various types of selection to alter livestock populations. Current selection strategies are little different, except our technologies for selection have become more powerful. Genetic resources at the breed level have been in and out of favour over time. These resources are the raw materials used to manipulate populations, and therefore, they are critical to the past and future success of the livestock sector. With increasing ability to rapidly change genetic composition of livestock populations, the conservation of these genetic resources becomes more critical. Globally, awareness of the need to steward genetic resources has increased. A growing number of countries have embarked on large scale conservation efforts by using in situ, ex situ (gene banking), or both approaches. Gene banking efforts have substantially increased and data suggest that gene banks are successfully capturing genetic diversity for research or industry use. It is also noteworthy that both industry and the research community are utilizing gene bank holdings. As pressures grow to meet consumer demands and potential changes in production systems, the linkage between selection goals and genetic conservation will increase as a mechanism to facilitate continued livestock sector development. © 2012 Blackwell Verlag GmbH.

Prospects and challenges for the conservation of farm animal genomic resources, 2015-2025

PubMed Central

Bruford, Michael W.; Ginja, Catarina; Hoffmann, Irene; Joost, Stéphane; Orozco-terWengel, Pablo; Alberto, Florian J.; Amaral, Andreia J.; Barbato, Mario; Biscarini, Filippo; Colli, Licia; Costa, Mafalda; Curik, Ino; Duruz, Solange; Ferenčaković, Maja; Fischer, Daniel; Fitak, Robert; Groeneveld, Linn F.; Hall, Stephen J. G.; Hanotte, Olivier; Hassan, Faiz-ul; Helsen, Philippe; Iacolina, Laura; Kantanen, Juha; Leempoel, Kevin; Lenstra, Johannes A.; Ajmone-Marsan, Paolo; Masembe, Charles; Megens, Hendrik-Jan; Miele, Mara; Neuditschko, Markus; Nicolazzi, Ezequiel L.; Pompanon, François; Roosen, Jutta; Sevane, Natalia; Smetko, Anamarija; Štambuk, Anamaria; Streeter, Ian; Stucki, Sylvie; Supakorn, China; Telo Da Gama, Luis; Tixier-Boichard, Michèle; Wegmann, Daniel; Zhan, Xiangjiang

2015-01-01

Livestock conservation practice is changing rapidly in light of policy developments, climate change and diversifying market demands. The last decade has seen a step change in technology and analytical approaches available to define, manage and conserve Farm Animal Genomic Resources (FAnGR). However, these rapid changes pose challenges for FAnGR conservation in terms of technological continuity, analytical capacity and integrative methodologies needed to fully exploit new, multidimensional data. The final conference of the ESF Genomic Resources program aimed to address these interdisciplinary problems in an attempt to contribute to the agenda for research and policy development directions during the coming decade. By 2020, according to the Convention on Biodiversity's Aichi Target 13, signatories should ensure that “…the genetic diversity of …farmed and domesticated animals and of wild relatives …is maintained, and strategies have been developed and implemented for minimizing genetic erosion and safeguarding their genetic diversity.” However, the real extent of genetic erosion is very difficult to measure using current data. Therefore, this challenging target demands better coverage, understanding and utilization of genomic and environmental data, the development of optimized ways to integrate these data with social and other sciences and policy analysis to enable more flexible, evidence-based models to underpin FAnGR conservation. At the conference, we attempted to identify the most important problems for effective livestock genomic resource conservation during the next decade. Twenty priority questions were identified that could be broadly categorized into challenges related to methodology, analytical approaches, data management and conservation. It should be acknowledged here that while the focus of our meeting was predominantly around genetics, genomics and animal science, many of the practical challenges facing conservation of genomic resources are societal in origin and are predicated on the value (e.g., socio-economic and cultural) of these resources to farmers, rural communities and society as a whole. The overall conclusion is that despite the fact that the livestock sector has been relatively well-organized in the application of genetic methodologies to date, there is still a large gap between the current state-of-the-art in the use of tools to characterize genomic resources and its application to many non-commercial and local breeds, hampering the consistent utilization of genetic and genomic data as indicators of genetic erosion and diversity. The livestock genomic sector therefore needs to make a concerted effort in the coming decade to enable to the democratization of the powerful tools that are now at its disposal, and to ensure that they are applied in the context of breed conservation as well as development. PMID:26539210

Prospects and challenges for the conservation of farm animal genomic resources, 2015-2025.

PubMed

Bruford, Michael W; Ginja, Catarina; Hoffmann, Irene; Joost, Stéphane; Orozco-terWengel, Pablo; Alberto, Florian J; Amaral, Andreia J; Barbato, Mario; Biscarini, Filippo; Colli, Licia; Costa, Mafalda; Curik, Ino; Duruz, Solange; Ferenčaković, Maja; Fischer, Daniel; Fitak, Robert; Groeneveld, Linn F; Hall, Stephen J G; Hanotte, Olivier; Hassan, Faiz-Ul; Helsen, Philippe; Iacolina, Laura; Kantanen, Juha; Leempoel, Kevin; Lenstra, Johannes A; Ajmone-Marsan, Paolo; Masembe, Charles; Megens, Hendrik-Jan; Miele, Mara; Neuditschko, Markus; Nicolazzi, Ezequiel L; Pompanon, François; Roosen, Jutta; Sevane, Natalia; Smetko, Anamarija; Štambuk, Anamaria; Streeter, Ian; Stucki, Sylvie; Supakorn, China; Telo Da Gama, Luis; Tixier-Boichard, Michèle; Wegmann, Daniel; Zhan, Xiangjiang

2015-01-01

Livestock conservation practice is changing rapidly in light of policy developments, climate change and diversifying market demands. The last decade has seen a step change in technology and analytical approaches available to define, manage and conserve Farm Animal Genomic Resources (FAnGR). However, these rapid changes pose challenges for FAnGR conservation in terms of technological continuity, analytical capacity and integrative methodologies needed to fully exploit new, multidimensional data. The final conference of the ESF Genomic Resources program aimed to address these interdisciplinary problems in an attempt to contribute to the agenda for research and policy development directions during the coming decade. By 2020, according to the Convention on Biodiversity's Aichi Target 13, signatories should ensure that "…the genetic diversity of …farmed and domesticated animals and of wild relatives …is maintained, and strategies have been developed and implemented for minimizing genetic erosion and safeguarding their genetic diversity." However, the real extent of genetic erosion is very difficult to measure using current data. Therefore, this challenging target demands better coverage, understanding and utilization of genomic and environmental data, the development of optimized ways to integrate these data with social and other sciences and policy analysis to enable more flexible, evidence-based models to underpin FAnGR conservation. At the conference, we attempted to identify the most important problems for effective livestock genomic resource conservation during the next decade. Twenty priority questions were identified that could be broadly categorized into challenges related to methodology, analytical approaches, data management and conservation. It should be acknowledged here that while the focus of our meeting was predominantly around genetics, genomics and animal science, many of the practical challenges facing conservation of genomic resources are societal in origin and are predicated on the value (e.g., socio-economic and cultural) of these resources to farmers, rural communities and society as a whole. The overall conclusion is that despite the fact that the livestock sector has been relatively well-organized in the application of genetic methodologies to date, there is still a large gap between the current state-of-the-art in the use of tools to characterize genomic resources and its application to many non-commercial and local breeds, hampering the consistent utilization of genetic and genomic data as indicators of genetic erosion and diversity. The livestock genomic sector therefore needs to make a concerted effort in the coming decade to enable to the democratization of the powerful tools that are now at its disposal, and to ensure that they are applied in the context of breed conservation as well as development.

Genetic counseling services and development of training programs in Malaysia.

PubMed

Lee, Juliana Mei-Har; Thong, Meow-Keong

2013-12-01

Genetic counseling service is urgently required in developing countries. In Malaysia, the first medical genetic service was introduced in 1994 at one of the main teaching hospitals in Kuala Lumpur. Two decades later, the medical genetic services have improved with the availability of genetic counseling, genetic testing and diagnosis, for both paediatric conditions and adult-onset inherited conditions, at four main centers of medical genetic services in Malaysia. Prenatal diagnosis services and assisted reproductive technologies are available at tertiary centres and private medical facilities. Positive developments include governmental recognition of Clinical Genetics as a subspecialty, increased funding for genetics services, development of medical ethics guidelines, and establishment of support groups. However, the country lacked qualified genetic counselors. Proposals were presented to policy-makers to develop genetic counseling courses. Challenges encountered included limited resources and public awareness, ethical dilemmas such as religious and social issues and inadequate genetic health professionals especially genetic counselors.

Diversity captured in the USDA-ARS National Plant Germplasm System apple core collection

USDA-ARS?s Scientific Manuscript database

Core collections have been used widely in genetic resources to provide a representative and compact sample to use in breeding evaluation. In the 1990s a core set was developed by the USDA-ARS Plant Genetic Resources Unit (PGRU) in Geneva, NY. Using data available at the time, a core set was develo...

Mouse Genome Informatics (MGI) Resource: Genetic, Genomic, and Biological Knowledgebase for the Laboratory Mouse.

PubMed

Eppig, Janan T

2017-07-01

The Mouse Genome Informatics (MGI) Resource supports basic, translational, and computational research by providing high-quality, integrated data on the genetics, genomics, and biology of the laboratory mouse. MGI serves a strategic role for the scientific community in facilitating biomedical, experimental, and computational studies investigating the genetics and processes of diseases and enabling the development and testing of new disease models and therapeutic interventions. This review describes the nexus of the body of growing genetic and biological data and the advances in computer technology in the late 1980s, including the World Wide Web, that together launched the beginnings of MGI. MGI develops and maintains a gold-standard resource that reflects the current state of knowledge, provides semantic and contextual data integration that fosters hypothesis testing, continually develops new and improved tools for searching and analysis, and partners with the scientific community to assure research data needs are met. Here we describe one slice of MGI relating to the development of community-wide large-scale mutagenesis and phenotyping projects and introduce ways to access and use these MGI data. References and links to additional MGI aspects are provided. © The Author 2017. Published by Oxford University Press.

Mouse Genome Informatics (MGI) Resource: Genetic, Genomic, and Biological Knowledgebase for the Laboratory Mouse

PubMed Central

Eppig, Janan T.

2017-01-01

Abstract The Mouse Genome Informatics (MGI) Resource supports basic, translational, and computational research by providing high-quality, integrated data on the genetics, genomics, and biology of the laboratory mouse. MGI serves a strategic role for the scientific community in facilitating biomedical, experimental, and computational studies investigating the genetics and processes of diseases and enabling the development and testing of new disease models and therapeutic interventions. This review describes the nexus of the body of growing genetic and biological data and the advances in computer technology in the late 1980s, including the World Wide Web, that together launched the beginnings of MGI. MGI develops and maintains a gold-standard resource that reflects the current state of knowledge, provides semantic and contextual data integration that fosters hypothesis testing, continually develops new and improved tools for searching and analysis, and partners with the scientific community to assure research data needs are met. Here we describe one slice of MGI relating to the development of community-wide large-scale mutagenesis and phenotyping projects and introduce ways to access and use these MGI data. References and links to additional MGI aspects are provided. PMID:28838066

A Toolkit for bulk PCR-based marker design from next-generation sequence data: application for development of a framework linkage map in bulb onion (Allium cepa L.)

PubMed Central

2012-01-01

Background Although modern sequencing technologies permit the ready detection of numerous DNA sequence variants in any organisms, converting such information to PCR-based genetic markers is hampered by a lack of simple, scalable tools. Onion is an example of an under-researched crop with a complex, heterozygous genome where genome-based research has previously been hindered by limited sequence resources and genetic markers. Results We report the development of generic tools for large-scale web-based PCR-based marker design in the Galaxy bioinformatics framework, and their application for development of next-generation genetics resources in a wide cross of bulb onion (Allium cepa L.). Transcriptome sequence resources were developed for the homozygous doubled-haploid bulb onion line ‘CUDH2150’ and the genetically distant Indian landrace ‘Nasik Red’, using 454™ sequencing of normalised cDNA libraries of leaf and shoot. Read mapping of ‘Nasik Red’ reads onto ‘CUDH2150’ assemblies revealed 16836 indel and SNP polymorphisms that were mined for portable PCR-based marker development. Tools for detection of restriction polymorphisms and primer set design were developed in BioPython and adapted for use in the Galaxy workflow environment, enabling large-scale and targeted assay design. Using PCR-based markers designed with these tools, a framework genetic linkage map of over 800cM spanning all chromosomes was developed in a subset of 93 F2 progeny from a very large F2 family developed from the ‘Nasik Red’ x ‘CUDH2150’ inter-cross. The utility of tools and genetic resources developed was tested by designing markers to transcription factor-like polymorphic sequences. Bin mapping these markers using a subset of 10 progeny confirmed the ability to place markers within 10 cM bins, enabling increased efficiency in marker assignment and targeted map refinement. The major genetic loci conditioning red bulb colour (R) and fructan content (Frc) were located on this map by QTL analysis. Conclusions The generic tools developed for the Galaxy environment enable rapid development of sets of PCR assays targeting sequence variants identified from Illumina and 454 sequence data. They enable non-specialist users to validate and exploit large volumes of next-generation sequence data using basic equipment. PMID:23157543

A toolkit for bulk PCR-based marker design from next-generation sequence data: application for development of a framework linkage map in bulb onion (Allium cepa L.).

PubMed

Baldwin, Samantha; Revanna, Roopashree; Thomson, Susan; Pither-Joyce, Meeghan; Wright, Kathryn; Crowhurst, Ross; Fiers, Mark; Chen, Leshi; Macknight, Richard; McCallum, John A

2012-11-19

Although modern sequencing technologies permit the ready detection of numerous DNA sequence variants in any organisms, converting such information to PCR-based genetic markers is hampered by a lack of simple, scalable tools. Onion is an example of an under-researched crop with a complex, heterozygous genome where genome-based research has previously been hindered by limited sequence resources and genetic markers. We report the development of generic tools for large-scale web-based PCR-based marker design in the Galaxy bioinformatics framework, and their application for development of next-generation genetics resources in a wide cross of bulb onion (Allium cepa L.). Transcriptome sequence resources were developed for the homozygous doubled-haploid bulb onion line 'CUDH2150' and the genetically distant Indian landrace 'Nasik Red', using 454™ sequencing of normalised cDNA libraries of leaf and shoot. Read mapping of 'Nasik Red' reads onto 'CUDH2150' assemblies revealed 16836 indel and SNP polymorphisms that were mined for portable PCR-based marker development. Tools for detection of restriction polymorphisms and primer set design were developed in BioPython and adapted for use in the Galaxy workflow environment, enabling large-scale and targeted assay design. Using PCR-based markers designed with these tools, a framework genetic linkage map of over 800cM spanning all chromosomes was developed in a subset of 93 F(2) progeny from a very large F(2) family developed from the 'Nasik Red' x 'CUDH2150' inter-cross. The utility of tools and genetic resources developed was tested by designing markers to transcription factor-like polymorphic sequences. Bin mapping these markers using a subset of 10 progeny confirmed the ability to place markers within 10 cM bins, enabling increased efficiency in marker assignment and targeted map refinement. The major genetic loci conditioning red bulb colour (R) and fructan content (Frc) were located on this map by QTL analysis. The generic tools developed for the Galaxy environment enable rapid development of sets of PCR assays targeting sequence variants identified from Illumina and 454 sequence data. They enable non-specialist users to validate and exploit large volumes of next-generation sequence data using basic equipment.

Domestication to Crop Improvement: Genetic Resources for Sorghum and Saccharum (Andropogoneae)

PubMed Central

Dillon, Sally L.; Shapter, Frances M.; Henry, Robert J.; Cordeiro, Giovanni; Izquierdo, Liz; Lee, L. Slade

2007-01-01

Background Both sorghum (Sorghum bicolor) and sugarcane (Saccharum officinarum) are members of the Andropogoneae tribe in the Poaceae and are each other's closest relatives amongst cultivated plants. Both are relatively recent domesticates and comparatively little of the genetic potential of these taxa and their wild relatives has been captured by breeding programmes to date. This review assesses the genetic gains made by plant breeders since domestication and the progress in the characterization of genetic resources and their utilization in crop improvement for these two related species. Genetic Resources The genome of sorghum has recently been sequenced providing a great boost to our knowledge of the evolution of grass genomes and the wealth of diversity within S. bicolor taxa. Molecular analysis of the Sorghum genus has identified close relatives of S. bicolor with novel traits, endosperm structure and composition that may be used to expand the cultivated gene pool. Mutant populations (including TILLING populations) provide a useful addition to genetic resources for this species. Sugarcane is a complex polyploid with a large and variable number of copies of each gene. The wild relatives of sugarcane represent a reservoir of genetic diversity for use in sugarcane improvement. Techniques for quantitative molecular analysis of gene or allele copy number in this genetically complex crop have been developed. SNP discovery and mapping in sugarcane has been advanced by the development of high-throughput techniques for ecoTILLING in sugarcane. Genetic linkage maps of the sugarcane genome are being improved for use in breeding selection. The improvement of both sorghum and sugarcane will be accelerated by the incorporation of more diverse germplasm into the domesticated gene pools using molecular tools and the improved knowledge of these genomes. PMID:17766842

'RetinoGenetics': a comprehensive mutation database for genes related to inherited retinal degeneration.

PubMed

Ran, Xia; Cai, Wei-Jun; Huang, Xiu-Feng; Liu, Qi; Lu, Fan; Qu, Jia; Wu, Jinyu; Jin, Zi-Bing

2014-01-01

Inherited retinal degeneration (IRD), a leading cause of human blindness worldwide, is exceptionally heterogeneous with clinical heterogeneity and genetic variety. During the past decades, tremendous efforts have been made to explore the complex heterogeneity, and massive mutations have been identified in different genes underlying IRD with the significant advancement of sequencing technology. In this study, we developed a comprehensive database, 'RetinoGenetics', which contains informative knowledge about all known IRD-related genes and mutations for IRD. 'RetinoGenetics' currently contains 4270 mutations in 186 genes, with detailed information associated with 164 phenotypes from 934 publications and various types of functional annotations. Then extensive annotations were performed to each gene using various resources, including Gene Ontology, KEGG pathways, protein-protein interaction, mutational annotations and gene-disease network. Furthermore, by using the search functions, convenient browsing ways and intuitive graphical displays, 'RetinoGenetics' could serve as a valuable resource for unveiling the genetic basis of IRD. Taken together, 'RetinoGenetics' is an integrative, informative and updatable resource for IRD-related genetic predispositions. Database URL: http://www.retinogenetics.org/. © The Author(s) 2014. Published by Oxford University Press.

Drosophila Genetic Resource and Stock Center; The National BioResource Project.

PubMed

Yamamoto, Masa-Toshi

2010-01-01

The fruit fly, Drosophila melanogaster, is not categorized as a laboratory animal, but it is recognised as one of the most important model organisms for basic biology, life science, and biomedical research. This tiny fly continues to occupy a core place in genetics and genomic approaches to studies of biology and medicine. The basic principles of genetics, including the variations of phenotypes, mutations, genetic linkage, meiotic chromosome segregation, chromosome aberrations, recombination, and precise mapping of genes by genetic as well as cytological means, were all derived from studies of Drosophila. Recombinant DNA technology was developed in the 1970s and Drosophila DNA was the first among multicellular organisms to be cloned. It provided a detailed characterization of genes in combination of classical cytogenetic data. Drosophila thus became the pioneering model organism for various fields of life science research into multicellular organisms. Here, I briefly describe the history of Drosophila research and provide a few examples of the application of the abundant genetic resources of Drosophila to basic biology and medical investigations. A Japanese national project, the National BioResource Project (NBRP) for collection, maintainance, and provision of Drosophila resources, that is well known and admired by researchers in other countries as an important project, is also briefly described.

Multiple Models for Rosaceae Genomics[OA

PubMed Central

Shulaev, Vladimir; Korban, Schuyler S.; Sosinski, Bryon; Abbott, Albert G.; Aldwinckle, Herb S.; Folta, Kevin M.; Iezzoni, Amy; Main, Dorrie; Arús, Pere; Dandekar, Abhaya M.; Lewers, Kim; Brown, Susan K.; Davis, Thomas M.; Gardiner, Susan E.; Potter, Daniel; Veilleux, Richard E.

2008-01-01

The plant family Rosaceae consists of over 100 genera and 3,000 species that include many important fruit, nut, ornamental, and wood crops. Members of this family provide high-value nutritional foods and contribute desirable aesthetic and industrial products. Most rosaceous crops have been enhanced by human intervention through sexual hybridization, asexual propagation, and genetic improvement since ancient times, 4,000 to 5,000 B.C. Modern breeding programs have contributed to the selection and release of numerous cultivars having significant economic impact on the U.S. and world markets. In recent years, the Rosaceae community, both in the United States and internationally, has benefited from newfound organization and collaboration that have hastened progress in developing genetic and genomic resources for representative crops such as apple (Malus spp.), peach (Prunus spp.), and strawberry (Fragaria spp.). These resources, including expressed sequence tags, bacterial artificial chromosome libraries, physical and genetic maps, and molecular markers, combined with genetic transformation protocols and bioinformatics tools, have rendered various rosaceous crops highly amenable to comparative and functional genomics studies. This report serves as a synopsis of the resources and initiatives of the Rosaceae community, recent developments in Rosaceae genomics, and plans to apply newly accumulated knowledge and resources toward breeding and crop improvement. PMID:18487361

The Genomic and Genetic Toolbox of the Teleost Medaka (Oryzias latipes)

PubMed Central

Kirchmaier, Stephan; Naruse, Kiyoshi; Wittbrodt, Joachim; Loosli, Felix

2015-01-01

The Japanese medaka, Oryzias latipes, is a vertebrate teleost model with a long history of genetic research. A number of unique features and established resources distinguish medaka from other vertebrate model systems. A large number of laboratory strains from different locations are available. Due to a high tolerance to inbreeding, many highly inbred strains have been established, thus providing a rich resource for genetic studies. Furthermore, closely related species native to different habitats in Southeast Asia permit comparative evolutionary studies. The transparency of embryos, larvae, and juveniles allows a detailed in vivo analysis of development. New tools to study diverse aspects of medaka biology are constantly being generated. Thus, medaka has become an important vertebrate model organism to study development, behavior, and physiology. In this review, we provide a comprehensive overview of established genetic and molecular-genetic tools that render medaka fish a full-fledged vertebrate system. PMID:25855651

Establishing the A. E. Watkins landrace cultivar collection as a resource for systematic gene discovery in bread wheat.

PubMed

Wingen, Luzie U; Orford, Simon; Goram, Richard; Leverington-Waite, Michelle; Bilham, Lorelei; Patsiou, Theofania S; Ambrose, Mike; Dicks, Jo; Griffiths, Simon

2014-08-01

A high level of genetic diversity was found in the A. E. Watkins bread wheat landrace collection. Genotypic information was used to determine the population structure and to develop germplasm resources. In the 1930s A. E. Watkins acquired landrace cultivars of bread wheat (Triticum aestivum L.) from official channels of the board of Trade in London, many of which originated from local markets in 32 countries. The geographic distribution of the 826 landrace cultivars of the current collection, here called the Watkins collection, covers many Asian and European countries and some from Africa. The cultivars were genotyped with 41 microsatellite markers in order to investigate the genetic diversity and population structure of the collection. A high level of genetic diversity was found, higher than in a collection of modern European winter bread wheat varieties from 1945 to 2000. Furthermore, although weak, the population structure of the Watkins collection reveals nine ancestral geographical groupings. An exchange of genetic material between ancestral groups before commercial wheat-breeding started would be a possible explanation for this. The increased knowledge regarding the diversity of the Watkins collection was used to develop resources for wheat research and breeding, one of them a core set, which captures the majority of the genetic diversity detected. The understanding of genetic diversity and population structure together with the availability of breeding resources should help to accelerate the detection of new alleles in the Watkins collection.

A Genomic Resource for the Development, Improvement, and Exploitation of Sorghum for Bioenergy.

PubMed

Brenton, Zachary W; Cooper, Elizabeth A; Myers, Mathew T; Boyles, Richard E; Shakoor, Nadia; Zielinski, Kelsey J; Rauh, Bradley L; Bridges, William C; Morris, Geoffrey P; Kresovich, Stephen

2016-09-01

With high productivity and stress tolerance, numerous grass genera of the Andropogoneae have emerged as candidates for bioenergy production. To optimize these candidates, research examining the genetic architecture of yield, carbon partitioning, and composition is required to advance breeding objectives. Significant progress has been made developing genetic and genomic resources for Andropogoneae, and advances in comparative and computational genomics have enabled research examining the genetic basis of photosynthesis, carbon partitioning, composition, and sink strength. To provide a pivotal resource aimed at developing a comparative understanding of key bioenergy traits in the Andropogoneae, we have established and characterized an association panel of 390 racially, geographically, and phenotypically diverse Sorghum bicolor accessions with 232,303 genetic markers. Sorghum bicolor was selected because of its genomic simplicity, phenotypic diversity, significant genomic tools, and its agricultural productivity and resilience. We have demonstrated the value of sorghum as a functional model for candidate gene discovery for bioenergy Andropogoneae by performing genome-wide association analysis for two contrasting phenotypes representing key components of structural and non-structural carbohydrates. We identified potential genes, including a cellulase enzyme and a vacuolar transporter, associated with increased non-structural carbohydrates that could lead to bioenergy sorghum improvement. Although our analysis identified genes with potentially clear functions, other candidates did not have assigned functions, suggesting novel molecular mechanisms for carbon partitioning traits. These results, combined with our characterization of phenotypic and genetic diversity and the public accessibility of each accession and genomic data, demonstrate the value of this resource and provide a foundation for future improvement of sorghum and related grasses for bioenergy production. Copyright © 2016 by the Genetics Society of America.

Population Genetic Structure of Glycyrrhiza inflata B. (Fabaceae) Is Shaped by Habitat Fragmentation, Water Resources and Biological Characteristics.

PubMed

Yang, Lulu; Chen, Jianjun; Hu, Weiming; Yang, Tianshun; Zhang, Yanjun; Yukiyoshi, Tamura; Zhou, Yanyang; Wang, Ying

2016-01-01

Habitat fragmentation, water resources and biological characteristics are important factors that shape the genetic structure and geographical distribution of desert plants. Analysis of the relationships between these factors and population genetic variation should help to determine the evolutionary potential and conservation strategies for genetic resources for desert plant populations. As a traditional Chinese herb, Glycyrrhiza inflata B. (Fabaceae) is restricted to the fragmented desert habitat in China and has undergone a dramatic decline due to long-term over-excavation. Determining the genetic structure of the G. inflata population and identifying a core collection could help with the development of strategies to conserve this species. We investigated the genetic variation of 25 G. inflata populations based on microsatellite markers. A high level of population genetic divergence (FST = 0.257), population bottlenecks, reduced gene flow and moderate genetic variation (HE = 0.383) were detected. The genetic distances between the populations significantly correlated with the geographical distances, and this suggests that habitat fragmentation has driven a special genetic structure of G. inflata in China through isolation by distance. STRUCTURE analysis showed that G. inflata populations were structured into three clusters and that the populations belonged to multiple water systems, which suggests that water resources were related to the genetic structure of G. inflata. In addition, the biological characteristics of the perennial species G. inflata, such as its long-lived seeds, asexual reproduction, and oasis ecology, may be related to its resistance to habitat fragmentation. A core collection of G. inflata, that included 57 accessions was further identified, which captured the main allelic diversity of G. inflata. Recent habitat fragmentation has accelerated genetic divergence. The population genetic structure of G. inflata has been shaped by habitat fragmentation, water resources and biological characteristics. This genetic information and core collection will facilitate the conservation of wild germplasm and breeding of this Chinese medicinal plant.

Population Genetic Structure of Glycyrrhiza inflata B. (Fabaceae) Is Shaped by Habitat Fragmentation, Water Resources and Biological Characteristics

PubMed Central

Yang, Lulu; Chen, Jianjun; Hu, Weiming; Yang, Tianshun; Zhang, Yanjun; Yukiyoshi, Tamura; Zhou, Yanyang; Wang, Ying

2016-01-01

Background Habitat fragmentation, water resources and biological characteristics are important factors that shape the genetic structure and geographical distribution of desert plants. Analysis of the relationships between these factors and population genetic variation should help to determine the evolutionary potential and conservation strategies for genetic resources for desert plant populations. As a traditional Chinese herb, Glycyrrhiza inflata B. (Fabaceae) is restricted to the fragmented desert habitat in China and has undergone a dramatic decline due to long-term over-excavation. Determining the genetic structure of the G. inflata population and identifying a core collection could help with the development of strategies to conserve this species. Results We investigated the genetic variation of 25 G. inflata populations based on microsatellite markers. A high level of population genetic divergence (FST = 0.257), population bottlenecks, reduced gene flow and moderate genetic variation (HE = 0.383) were detected. The genetic distances between the populations significantly correlated with the geographical distances, and this suggests that habitat fragmentation has driven a special genetic structure of G. inflata in China through isolation by distance. STRUCTURE analysis showed that G. inflata populations were structured into three clusters and that the populations belonged to multiple water systems, which suggests that water resources were related to the genetic structure of G. inflata. In addition, the biological characteristics of the perennial species G. inflata, such as its long-lived seeds, asexual reproduction, and oasis ecology, may be related to its resistance to habitat fragmentation. A core collection of G. inflata, that included 57 accessions was further identified, which captured the main allelic diversity of G. inflata. Conclusions Recent habitat fragmentation has accelerated genetic divergence. The population genetic structure of G. inflata has been shaped by habitat fragmentation, water resources and biological characteristics. This genetic information and core collection will facilitate the conservation of wild germplasm and breeding of this Chinese medicinal plant. PMID:27711241

Juridical and sociocultural problems on the definition of a law concerning property, usage and access to genetic resources in Colombia.

PubMed

Calle, R

1996-04-01

The property, usage, and access to genetic resources, is today one of the primary topics in international business, as a result of the strategic importance of the resources for the biotechnology industry. Internationally, the sovereignty that each country has over its natural patrimony is recognized. However, the new laws of international marketing have obligated countries in the process of development, such as Colombia, to adopt and copy a concept of intellectual property on living resources that does not have anything to do with the country's sociocultural identity, and sometimes even does not take into account its material enjoyment. The new juridical movement that treats genetic resources as private property produces a cultural conflict between indigenous populations, Afro-Americans and peasants, because for them the genetic resources are an element of community life. In these communities, knowledge is freely transmitted; it is an understanding that they have to conserve their agricultural customs and the relationship that they have with the environment. They do not recognize the term "property' according to patenting laws. These elements have to be considered, respected, and guaranteed in the laws that recognize the genetic resources in the country. On the other hand, not even countries that are pioneers in biotechnological development can adopt a concept about patents that is in agreement with the particularities that the living materials possess. This is obviously the reason for the numerous discussions on the legal interpretation, as well as complicated debates in court. Confronting that situation, there are countries rich in biodiversity, such as Colombia, but which do not have a proper concept and are not economically strong in the international context. These countries have to copy inadequate protection policies that do not take into account all their rights. This paper describes some of the technical, juridical, and sociocultural difficulties which Colombia has to confront, in order to set a guideline on patenting living organisms, and on the access and usage of the genetic resources.

ILDgenDB: integrated genetic knowledge resource for interstitial lung diseases (ILDs).

PubMed

Mishra, Smriti; Shah, Mohammad I; Sarkar, Malay; Asati, Nimisha; Rout, Chittaranjan

2018-01-01

Interstitial lung diseases (ILDs) are a diverse group of ∼200 acute and chronic pulmonary disorders that are characterized by variable amounts of inflammation, fibrosis and architectural distortion with substantial morbidity and mortality. Inaccurate and delayed diagnoses increase the risk, especially in developing countries. Studies have indicated the significant roles of genetic elements in ILDs pathogenesis. Therefore, the first genetic knowledge resource, ILDgenDB, has been developed with an objective to provide ILDs genetic data and their integrated analyses for the better understanding of disease pathogenesis and identification of diagnostics-based biomarkers. This resource contains literature-curated disease candidate genes (DCGs) enriched with various regulatory elements that have been generated using an integrated bioinformatics workflow of databases searches, literature-mining and DCGs-microRNA (miRNAs)-single nucleotide polymorphisms (SNPs) association analyses. To provide statistical significance to disease-gene association, ILD-specificity index and hypergeomatric test scores were also incorporated. Association analyses of miRNAs, SNPs and pathways responsible for the pathogenesis of different sub-classes of ILDs were also incorporated. Manually verified 299 DCGs and their significant associations with 1932 SNPs, 2966 miRNAs and 9170 miR-polymorphisms were also provided. Furthermore, 216 literature-mined and proposed biomarkers were identified. The ILDgenDB resource provides user-friendly browsing and extensive query-based information retrieval systems. Additionally, this resource also facilitates graphical view of predicted DCGs-SNPs/miRNAs and literature associated DCGs-ILDs interactions for each ILD to facilitate efficient data interpretation. Outcomes of analyses suggested the significant involvement of immune system and defense mechanisms in ILDs pathogenesis. This resource may potentially facilitate genetic-based disease monitoring and diagnosis.Database URL: http://14.139.240.55/ildgendb/index.php.

DEVELOPMENT OF EPIC GENETIC MARKERS AND THE UTILITY OF A MULTI-LOCUS, MULTI-TAXA PHYLOGEOGRAPHICAL APPROACH TO EXAMINING PATTERNS OF GENETIC DIVERSITY

EPA Science Inventory

Use of population genetic measures for assessing the structure of natural populations and the condition of biological resources has increased steadily since the 1970's. Traditionally, genetic diversity within and among geographic areas is assessed based on a one-time sampling of...

A Genomic Resource for the Development, Improvement, and Exploitation of Sorghum for Bioenergy

PubMed Central

Brenton, Zachary W.; Cooper, Elizabeth A.; Myers, Mathew T.; Boyles, Richard E.; Shakoor, Nadia; Zielinski, Kelsey J.; Rauh, Bradley L.; Bridges, William C.; Morris, Geoffrey P.; Kresovich, Stephen

2016-01-01

With high productivity and stress tolerance, numerous grass genera of the Andropogoneae have emerged as candidates for bioenergy production. To optimize these candidates, research examining the genetic architecture of yield, carbon partitioning, and composition is required to advance breeding objectives. Significant progress has been made developing genetic and genomic resources for Andropogoneae, and advances in comparative and computational genomics have enabled research examining the genetic basis of photosynthesis, carbon partitioning, composition, and sink strength. To provide a pivotal resource aimed at developing a comparative understanding of key bioenergy traits in the Andropogoneae, we have established and characterized an association panel of 390 racially, geographically, and phenotypically diverse Sorghum bicolor accessions with 232,303 genetic markers. Sorghum bicolor was selected because of its genomic simplicity, phenotypic diversity, significant genomic tools, and its agricultural productivity and resilience. We have demonstrated the value of sorghum as a functional model for candidate gene discovery for bioenergy Andropogoneae by performing genome-wide association analysis for two contrasting phenotypes representing key components of structural and non-structural carbohydrates. We identified potential genes, including a cellulase enzyme and a vacuolar transporter, associated with increased non-structural carbohydrates that could lead to bioenergy sorghum improvement. Although our analysis identified genes with potentially clear functions, other candidates did not have assigned functions, suggesting novel molecular mechanisms for carbon partitioning traits. These results, combined with our characterization of phenotypic and genetic diversity and the public accessibility of each accession and genomic data, demonstrate the value of this resource and provide a foundation for future improvement of sorghum and related grasses for bioenergy production. PMID:27356613

Permanent Genetic Resources added to Molecular Ecology Resources Database 1 December 2009–31 January 2010

USDA-ARS?s Scientific Manuscript database

This article documents the addition of 220 microsatellite marker loci to the Molecular Ecology Resources Database. Loci were developed for the following species: Allanblackia floribunda, Amblyraja radiata, Bactrocera cucurbitae, Brachycaudus helichrysi, Calopogonium mucunoides, Dissodactylus primiti...

Application of RAD Sequencing for Evaluating the Genetic Diversity of Domesticated Panax notoginseng (Araliaceae)

PubMed Central

Pan, Yuezhi; Wang, Xueqin; Sun, Guiling; Li, Fusheng; Gong, Xun

2016-01-01

Panax notoginseng, a traditional Chinese medicinal plant, has been cultivated and domesticated for approximately 400 years, mainly in Yunnan and Guangxi, two provinces in southwest China. This species was named according to cultivated rather than wild individuals, and no wild populations had been found until now. The genetic resources available on farms are important for both breeding practices and resource conservation. In the present study, the recently developed technology RADseq, which is based on next-generation sequencing, was used to analyze the genetic variation and differentiation of P. notoginseng. The nucleotide diversity and heterozygosity results indicated that P. notoginseng had low genetic diversity at both the species and population levels. Almost no genetic differentiation has been detected, and all populations were genetically similar due to strong gene flow and insufficient splitting time. Although the genetic diversity of P. notoginseng was low at both species and population levels, several traditional plantations had relatively high genetic diversity, as revealed by the He and π values and by the private allele numbers. These valuable genetic resources should be protected as soon as possible to facilitate future breeding projects. The possible geographical origin of Sanqi domestication was discussed based on the results of the genetic diversity analysis. PMID:27846268

Access and benefits sharing of genetic resources and associated traditional knowledge in northern Canada: understanding the legal environment and creating effective research agreements

PubMed Central

Geary, Janis; Jardine, Cynthia G.; Guebert, Jenilee; Bubela, Tania

2013-01-01

Background Research in northern Canada focused on Aboriginal peoples has historically benefited academia with little consideration for the people being researched or their traditional knowledge (TK). Although this attitude is changing, the complexity of TK makes it difficult to develop mechanisms to preserve and protect it. Protecting TK becomes even more important when outside groups become interested in using TK or materials with associated TK. In the latter category are genetic resources, which may have commercial value and are the focus of this article. Objective This article addresses access to and use of genetic resources and associated TK in the context of the historical power-imbalances in research relationships in Canadian north. Design Review. Results Research involving genetic resources and TK is becoming increasingly relevant in northern Canada. The legal framework related to genetic resources and the cultural shift of universities towards commercial goals in research influence the environment for negotiating research agreements. Current guidelines for research agreements do not offer appropriate guidelines to achieve mutual benefit, reflect unequal bargaining power or take the relationship between parties into account. Conclusions Relational contract theory may be a useful framework to address the social, cultural and legal hurdles inherent in creating research agreements. PMID:23986896

Access and benefits sharing of genetic resources and associated traditional knowledge in northern Canada: understanding the legal environment and creating effective research agreements.

PubMed

Geary, Janis; Jardine, Cynthia G; Guebert, Jenilee; Bubela, Tania

2013-01-01

Research in northern Canada focused on Aboriginal peoples has historically benefited academia with little consideration for the people being researched or their traditional knowledge (TK). Although this attitude is changing, the complexity of TK makes it difficult to develop mechanisms to preserve and protect it. Protecting TK becomes even more important when outside groups become interested in using TK or materials with associated TK. In the latter category are genetic resources, which may have commercial value and are the focus of this article. This article addresses access to and use of genetic resources and associated TK in the context of the historical power-imbalances in research relationships in Canadian north. Review. Research involving genetic resources and TK is becoming increasingly relevant in northern Canada. The legal framework related to genetic resources and the cultural shift of universities towards commercial goals in research influence the environment for negotiating research agreements. Current guidelines for research agreements do not offer appropriate guidelines to achieve mutual benefit, reflect unequal bargaining power or take the relationship between parties into account. Relational contract theory may be a useful framework to address the social, cultural and legal hurdles inherent in creating research agreements.

Genetics Home Reference: GM3 synthase deficiency

MedlinePlus

... GM3 synthase deficiency is characterized by recurrent seizures (epilepsy) and problems with brain development. Within the first ... Testing (1 link) Genetic Testing Registry: Amish infantile epilepsy syndrome Other Diagnosis and Management Resources (2 links) ...

Genetic Simulation Resources: a website for the registration and discovery of genetic data simulators

PubMed Central

Peng, Bo; Chen, Huann-Sheng; Mechanic, Leah E.; Racine, Ben; Clarke, John; Clarke, Lauren; Gillanders, Elizabeth; Feuer, Eric J.

2013-01-01

Summary: Many simulation methods and programs have been developed to simulate genetic data of the human genome. These data have been widely used, for example, to predict properties of populations retrospectively or prospectively according to mathematically intractable genetic models, and to assist the validation, statistical inference and power analysis of a variety of statistical models. However, owing to the differences in type of genetic data of interest, simulation methods, evolutionary features, input and output formats, terminologies and assumptions for different applications, choosing the right tool for a particular study can be a resource-intensive process that usually involves searching, downloading and testing many different simulation programs. Genetic Simulation Resources (GSR) is a website provided by the National Cancer Institute (NCI) that aims to help researchers compare and choose the appropriate simulation tools for their studies. This website allows authors of simulation software to register their applications and describe them with well-defined attributes, thus allowing site users to search and compare simulators according to specified features. Availability: http://popmodels.cancercontrol.cancer.gov/gsr. Contact: gsr@mail.nih.gov PMID:23435068

Market organization and animal genetic resource management: a revealed preference analysis of sheep pricing.

PubMed

Tindano, K; Moula, N; Leroy, P; Traoré, A; Antoine-Moussiaux, N

2017-10-01

Farm animal genetic resources are threatened worldwide. Participation in markets, while representing a crucial way out of poverty for many smallholders, affects genetic management choices with associated sustainability concerns. This paper proposes a contextualized study of the interactions between markets and animal genetic resources management, in the case of sheep markets in Ouagadougou, Burkina Faso. It focusses on the organization of marketing chains and the valuation of genetic characteristics by value chain actors. Marketing chain characterization was tackled through semi-structured interviews with 25 exporters and 15 butchers, both specialized in sheep. Moreover, revealed preference methods were applied to analyse the impact of animals' attributes on market pricing. Data were collected from 338 transactions during three different periods: Eid al-Adha, Christmas and New Year period, and a neutral period. The neutral period is understood as a period not close to any event likely to influence the demand for sheep. The results show that physical characteristics such as live weight, height at withers and coat colour have a strong influence on the animals' prices. Live weight has also had an increasing marginal impact on price. The different markets (local butcher, feasts, export market, sacrifices) represent distinct demands for genetic characteristics, entailing interesting consequences for animal genetic resource management. Any breeding programme should therefore take this diversity into account to allow this sector to contribute better to a sustainable development of the country.

Sharing the benefits of genetic resources: from biodiversity to human genetics.

PubMed

Schroeder, Doris; Lasén-Díaz, Carolina

2006-12-01

Benefit sharing aims to achieve an equitable exchange between the granting of access to a genetic resource and the provision of compensation. The Convention on Biological Diversity (CBD), adopted at the 1992 Earth Summit in Rio de Janeiro, is the only international legal instrument setting out obligations for sharing the benefits derived from the use of biodiversity. The CBD excludes human genetic resources from its scope, however, this article considers whether it should be expanded to include those resources, so as to enable research subjects to claim a share of the benefits to be negotiated on a case-by-case basis. Our conclusion on this question is: 'No, the CBD should not be expanded to include human genetic resources.' There are essential differences between human and non-human genetic resources, and, in the context of research on humans, an essentially fair exchange model is already available between the health care industry and research subjects. Those who contribute to research should receive benefits in the form of accessible new health care products and services, suitable for local health needs and linked to economic prosperity (e.g. jobs). When this exchange model does not apply, as is often the case in developing countries, individually negotiated benefit sharing agreements between researchers and research subjects should not be used as 'window dressing'. Instead, national governments should focus their finances on the best economic investment they could make; the investment in population health and health research as outlined by the World Health Organization's Commission on Macroeconomics and Health; whilst international barriers to such spending need to be removed.

Germplasm morgue or gold mine? Enhancing the value of plant genetic resource collections for plant breeding

USDA-ARS?s Scientific Manuscript database

Genetic diversity is the raw material that plant breeders require to develop cultivars that are productive, nutritious, pest and stress tolerant, and water and nutrient use efficient. The USDA-ARS National Plant Germplasm System (NPGS) contains a wealth of genetic diversity, including improved varie...

Setaria viridis as a Model System to Advance Millet Genetics and Genomics

PubMed Central

Huang, Pu; Shyu, Christine; Coelho, Carla P.; Cao, Yingying; Brutnell, Thomas P.

2016-01-01

Millet is a common name for a group of polyphyletic, small-seeded cereal crops that include pearl, finger and foxtail millet. Millet species are an important source of calories for many societies, often in developing countries. Compared to major cereal crops such as rice and maize, millets are generally better adapted to dry and hot environments. Despite their food security value, the genetic architecture of agronomically important traits in millets, including both morphological traits and climate resilience remains poorly studied. These complex traits have been challenging to dissect in large part because of the lack of sufficient genetic tools and resources. In this article, we review the phylogenetic relationship among various millet species and discuss the value of a genetic model system for millet research. We propose that a broader adoption of green foxtail (Setaria viridis) as a model system for millets could greatly accelerate the pace of gene discovery in the millets, and summarize available and emerging resources in S. viridis and its domesticated relative S. italica. These resources have value in forward genetics, reverse genetics and high throughput phenotyping. We describe methods and strategies to best utilize these resources to facilitate the genetic dissection of complex traits. We envision that coupling cutting-edge technologies and the use of S. viridis for gene discovery will accelerate genetic research in millets in general. This will enable strategies and provide opportunities to increase productivity, especially in the semi-arid tropics of Asia and Africa where millets are staple food crops. PMID:27965689

Setaria viridis as a Model System to Advance Millet Genetics and Genomics.

PubMed

Huang, Pu; Shyu, Christine; Coelho, Carla P; Cao, Yingying; Brutnell, Thomas P

2016-01-01

Millet is a common name for a group of polyphyletic, small-seeded cereal crops that include pearl, finger and foxtail millet. Millet species are an important source of calories for many societies, often in developing countries. Compared to major cereal crops such as rice and maize, millets are generally better adapted to dry and hot environments. Despite their food security value, the genetic architecture of agronomically important traits in millets, including both morphological traits and climate resilience remains poorly studied. These complex traits have been challenging to dissect in large part because of the lack of sufficient genetic tools and resources. In this article, we review the phylogenetic relationship among various millet species and discuss the value of a genetic model system for millet research. We propose that a broader adoption of green foxtail ( Setaria viridis ) as a model system for millets could greatly accelerate the pace of gene discovery in the millets, and summarize available and emerging resources in S. viridis and its domesticated relative S. italica . These resources have value in forward genetics, reverse genetics and high throughput phenotyping. We describe methods and strategies to best utilize these resources to facilitate the genetic dissection of complex traits. We envision that coupling cutting-edge technologies and the use of S. viridis for gene discovery will accelerate genetic research in millets in general. This will enable strategies and provide opportunities to increase productivity, especially in the semi-arid tropics of Asia and Africa where millets are staple food crops.

Behavioral genetics and taste

PubMed Central

Boughter, John D; Bachmanov, Alexander A

2007-01-01

This review focuses on behavioral genetic studies of sweet, umami, bitter and salt taste responses in mammals. Studies involving mouse inbred strain comparisons and genetic analyses, and their impact on elucidation of taste receptors and transduction mechanisms are discussed. Finally, the effect of genetic variation in taste responsiveness on complex traits such as drug intake is considered. Recent advances in development of genomic resources make behavioral genetics a powerful approach for understanding mechanisms of taste. PMID:17903279

Complex Genetic Effects on Early Vegetative Development Shape Resource Allocation Differences Between Arabidopsis lyrata Populations

PubMed Central

Remington, David L.; Leinonen, Päivi H.; Leppälä, Johanna; Savolainen, Outi

2013-01-01

Costs of reproduction due to resource allocation trade-offs have long been recognized as key forces in life history evolution, but little is known about their functional or genetic basis. Arabidopsis lyrata, a perennial relative of the annual model plant A. thaliana with a wide climatic distribution, has populations that are strongly diverged in resource allocation. In this study, we evaluated the genetic and functional basis for variation in resource allocation in a reciprocal transplant experiment, using four A. lyrata populations and F2 progeny from a cross between North Carolina (NC) and Norway parents, which had the most divergent resource allocation patterns. Local alleles at quantitative trait loci (QTL) at a North Carolina field site increased reproductive output while reducing vegetative growth. These QTL had little overlap with flowering date QTL. Structural equation models incorporating QTL genotypes and traits indicated that resource allocation differences result primarily from QTL effects on early vegetative growth patterns, with cascading effects on later vegetative and reproductive development. At a Norway field site, North Carolina alleles at some of the same QTL regions reduced survival and reproductive output components, but these effects were not associated with resource allocation trade-offs in the Norway environment. Our results indicate that resource allocation in perennial plants may involve important adaptive mechanisms largely independent of flowering time. Moreover, the contributions of resource allocation QTL to local adaptation appear to result from their effects on developmental timing and its interaction with environmental constraints, and not from simple models of reproductive costs. PMID:23979581

Diversity, genetic mapping, and signatures of domestication in the carrot (Daucus carota L.) genome, as revealed by Diversity Arrays Technology (DArT) markers

USDA-ARS?s Scientific Manuscript database

Carrot is one of the most economically important vegetables worldwide, however, genetic and genomic resources supporting carrot breeding remain limited. We developed a Diversity Arrays Technology (DArT) platform for wild and cultivated carrot and used it to investigate genetic diversity and to devel...

Genome-wide single nucleotide polymorphisms (SNPs) for a model invasive ascidian Botryllus schlosseri.

PubMed

Gao, Yangchun; Li, Shiguo; Zhan, Aibin

2018-04-01

Invasive species cause huge damages to ecology, environment and economy globally. The comprehensive understanding of invasion mechanisms, particularly genetic bases of micro-evolutionary processes responsible for invasion success, is essential for reducing potential damages caused by invasive species. The golden star tunicate, Botryllus schlosseri, has become a model species in invasion biology, mainly owing to its high invasiveness nature and small well-sequenced genome. However, the genome-wide genetic markers have not been well developed in this highly invasive species, thus limiting the comprehensive understanding of genetic mechanisms of invasion success. Using restriction site-associated DNA (RAD) tag sequencing, here we developed a high-quality resource of 14,119 out of 158,821 SNPs for B. schlosseri. These SNPs were relatively evenly distributed at each chromosome. SNP annotations showed that the majority of SNPs (63.20%) were located at intergenic regions, and 21.51% and 14.58% were located at introns and exons, respectively. In addition, the potential use of the developed SNPs for population genomics studies was primarily assessed, such as the estimate of observed heterozygosity (H O ), expected heterozygosity (H E ), nucleotide diversity (π), Wright's inbreeding coefficient (F IS ) and effective population size (Ne). Our developed SNP resource would provide future studies the genome-wide genetic markers for genetic and genomic investigations, such as genetic bases of micro-evolutionary processes responsible for invasion success.

Data mining for multiagent rules, strategies, and fuzzy decision tree structure

NASA Astrophysics Data System (ADS)

Smith, James F., III; Rhyne, Robert D., II; Fisher, Kristin

2002-03-01

A fuzzy logic based resource manager (RM) has been developed that automatically allocates electronic attack resources in real-time over many dissimilar platforms. Two different data mining algorithms have been developed to determine rules, strategies, and fuzzy decision tree structure. The first data mining algorithm uses a genetic algorithm as a data mining function and is called from an electronic game. The game allows a human expert to play against the resource manager in a simulated battlespace with each of the defending platforms being exclusively directed by the fuzzy resource manager and the attacking platforms being controlled by the human expert or operating autonomously under their own logic. This approach automates the data mining problem. The game automatically creates a database reflecting the domain expert's knowledge. It calls a data mining function, a genetic algorithm, for data mining of the database as required and allows easy evaluation of the information mined in the second step. The criterion for re- optimization is discussed as well as experimental results. Then a second data mining algorithm that uses a genetic program as a data mining function is introduced to automatically discover fuzzy decision tree structures. Finally, a fuzzy decision tree generated through this process is discussed.

Reprogenetics and pharmacogenetics: in whose best interests?

PubMed

Mackenzie, Robin

2005-06-01

Reprogenetics involves embryonic pre-implantation genetic diagnosis, provoking controversy over the creation of saviour siblings, eugenics and genetic enhancement. It will soon ascertain pharmacogenetic susceptibilities. Pharmacogenetics impacts upon public health initiatives underpinned by resource allocation constraints in that genetic epidemiological studies assist in administering health care resources and public health strategies. Knowing how likely sections of the population are to develop specific medical conditions so that lifestyle and environmental factors influencing these conditions can be targeted has the potential to save public money and improve public health. Aligning population groups with genetic susceptibilities with specific medications would enable cost-effective prescribing. Reprogenetics and pharmacogenetics also possess great commercial potential for nation states and biotechnology companies. Hence ethical legal safeguards for members of the public whose reproductive or genetic tissue is a research or health care resource are essential. Both legal measures such as informed consent and mechanisms for including the public in policy decisions over reprogenetics and pharmacogenetics must be rethought to ensure that they provide protection rather than function as rubber stamps which preclude deeper inquiry into justifications of projects.

A first genetic map of date palm (Phoenix dactylifera) reveals long-range genome structure conservation in the palms.

PubMed

Mathew, Lisa S; Spannagl, Manuel; Al-Malki, Ameena; George, Binu; Torres, Maria F; Al-Dous, Eman K; Al-Azwani, Eman K; Hussein, Emad; Mathew, Sweety; Mayer, Klaus F X; Mohamoud, Yasmin Ali; Suhre, Karsten; Malek, Joel A

2014-04-15

The date palm is one of the oldest cultivated fruit trees. It is critical in many ways to cultures in arid lands by providing highly nutritious fruit while surviving extreme heat and environmental conditions. Despite its importance from antiquity, few genetic resources are available for improving the productivity and development of the dioecious date palm. To date there has been no genetic map and no sex chromosome has been identified. Here we present the first genetic map for date palm and identify the putative date palm sex chromosome. We placed ~4000 markers on the map using nearly 1200 framework markers spanning a total of 1293 cM. We have integrated the genetic map, derived from the Khalas cultivar, with the draft genome and placed up to 19% of the draft genome sequence scaffolds onto linkage groups for the first time. This analysis revealed approximately ~1.9 cM/Mb on the map. Comparison of the date palm linkage groups revealed significant long-range synteny to oil palm. Analysis of the date palm sex-determination region suggests it is telomeric on linkage group 12 and recombination is not suppressed in the full chromosome. Based on a modified genotyping-by-sequencing approach we have overcome challenges due to lack of genetic resources and provide the first genetic map for date palm. Combined with the recent draft genome sequence of the same cultivar, this resource offers a critical new tool for date palm biotechnology, palm comparative genomics and a better understanding of sex chromosome development in the palms.

Setaria viridis as a Model System to Advance Millet Genetics and Genomics

DOE PAGES

Huang, Pu; Shyu, Christine; Coelho, Carla P.; ...

2016-11-28

Millet is a common name for a group of polyphyletic, small-seeded cereal crops that include pearl, finger and foxtail millet. Millet species are an important source of calories for many societies, often in developing countries. Compared to major cereal crops such as rice and maize, millets are generally better adapted to dry and hot environments. Yet despite their food security value, the genetic architecture of agronomically important traits in millets, including both morphological traits and climate resilience remains poorly studied. These complex traits have been challenging to dissect in large part because of the lack of sufficient genetic tools andmore » resources. In this article, we review the phylogenetic relationship among various millet species and discuss the value of a genetic model system for millet research. We propose that a broader adoption of green foxtail (Setaria viridis) as a model system for millets could greatly accelerate the pace of gene discovery in the millets, and summarize available and emerging resources in S. viridis and its domesticated relative S. italica. These resources have value in forward genetics, reverse genetics and high throughput phenotyping. We describe methods and strategies to best utilize these resources to facilitate the genetic dissection of complex traits. We envision that coupling cutting-edge technologies and the use of S. viridis for gene discovery will accelerate genetic research in millets in general. This will enable strategies and provide opportunities to increase productivity, especially in the semi-arid tropics of Asia and Africa where millets are staple food crops.« less

Setaria viridis as a Model System to Advance Millet Genetics and Genomics

DOE Office of Scientific and Technical Information (OSTI.GOV)

Huang, Pu; Shyu, Christine; Coelho, Carla P.

Millet is a common name for a group of polyphyletic, small-seeded cereal crops that include pearl, finger and foxtail millet. Millet species are an important source of calories for many societies, often in developing countries. Compared to major cereal crops such as rice and maize, millets are generally better adapted to dry and hot environments. Yet despite their food security value, the genetic architecture of agronomically important traits in millets, including both morphological traits and climate resilience remains poorly studied. These complex traits have been challenging to dissect in large part because of the lack of sufficient genetic tools andmore » resources. In this article, we review the phylogenetic relationship among various millet species and discuss the value of a genetic model system for millet research. We propose that a broader adoption of green foxtail (Setaria viridis) as a model system for millets could greatly accelerate the pace of gene discovery in the millets, and summarize available and emerging resources in S. viridis and its domesticated relative S. italica. These resources have value in forward genetics, reverse genetics and high throughput phenotyping. We describe methods and strategies to best utilize these resources to facilitate the genetic dissection of complex traits. We envision that coupling cutting-edge technologies and the use of S. viridis for gene discovery will accelerate genetic research in millets in general. This will enable strategies and provide opportunities to increase productivity, especially in the semi-arid tropics of Asia and Africa where millets are staple food crops.« less

Science and society: protecting crop genetic diversity for food security: political, ethical and technical challenges.

PubMed

Esquinas-Alcázar, José

2005-12-01

Crop genetic diversity - which is crucial for feeding humanity, for the environment and for sustainable development - is being lost at an alarming rate. Given the enormous interdependence of countries and generations on this genetic diversity, this loss raises critical socio-economic, ethical and political questions. The recent ratification of a binding international treaty, and the development of powerful new technologies to conserve and use resources more effectively, have raised expectations that must now be fulfilled.

Harnessing the sorghum genome sequence:development of a genome-wide microsattelite (SSR) resource for swift genetic mapping and map based cloning in sorghum

USDA-ARS?s Scientific Manuscript database

Sorghum is the second cereal crop to have a full genome completely sequenced (Nature (2009), 457:551). This achievement is widely recognized as a scientific milestone for grass genetics and genomics in general. However, the true worth of genetic information lies in translating the sequence informa...

A model of genetic variation for Pinus ponderosa in the Inland Northwest (U.S.A.): applications in gene resource management

Treesearch

Gerald Rehfeldt

1991-01-01

Models were developed to describe genetic variation among 201 seedling populations of Pinus ponderosa var. ponderosa in the Inland Northwest of the United States. Common-garden studies provided three variables Jhat reflected growth and development in field environments and three principal components of six variables that reflected patterns of shoot elongation....

Genetic Tool Development for a New Host for Biotechnology, the Thermotolerant Bacterium Bacillus coagulans▿ †

PubMed Central

Kovács, Ákos T.; van Hartskamp, Mariska; Kuipers, Oscar P.; van Kranenburg, Richard

2010-01-01

Bacillus coagulans has good potential as an industrial production organism for platform chemicals from renewable resources but has limited genetic tools available. Here, we present a targeted gene disruption system using the Cre-lox system, development of a LacZ reporter assay for monitoring gene transcription, and heterologous d-lactate dehydrogenase expression. PMID:20400555

Molecular identification of livestock breeds: a tool for modern conservation biology.

PubMed

Yaro, Mohammed; Munyard, Kylie A; Stear, Michael J; Groth, David M

2017-05-01

Global livestock genetic diversity includes all of the species, breeds and strains of domestic animals, and their variations. Although a recent census indicated that there were 40 species and over 8000 breeds of domestic animals; for the purpose of conservation biology the diversity between and within breeds rather than species is regarded to be of crucial importance. This domestic animal genetic diversity has developed through three main evolutionary events, from speciation (about 3 million years ago) through domestication (about 12000 years ago) to specialised breeding (starting about 200 years ago). These events and their impacts on global animal genetic resources have been well documented in the literature. The key importance of global domestic animal resources in terms of economic, scientific and cultural heritage has also been addressed. In spite of their importance, there is a growing number of reports on the alarming erosion of domestic animal genetic resources. This erosion of is happening in spite of several global conservation initiatives designed to mitigate it. Herein we discuss these conservation interventions and highlight their strengths and weaknesses. However, pivotal to the success of these conservation initiatives is the reliability of the genetic assignment of individual members to a target breed. Finally, we discuss the prospect of using improved breed identification methodologies to develop a reliable breed-specific molecular identification tool that is easily applicable to populations of livestock breeds in various ecosystems. These identification tools, when developed, will not only facilitate the regular monitoring of threatened or endangered breed populations, but also enhance the development of more efficient and sustainable livestock production systems. © 2016 Cambridge Philosophical Society.

Design and implementation of the cacao genome database

USDA-ARS?s Scientific Manuscript database

The Cacao Genome Database (CGD, www.cacaogenomedb.org) is being developed to provide a comprehensive data mining resource of genomic, genetic and breeding data for Theobroma cacao. Designed using Chado and a collection of Drupal modules, known as Tripal, CGD currently contains the genetically anchor...

Genetic and developing genomic resources in black raspberry

USDA-ARS?s Scientific Manuscript database

Breeding progress in black raspberry (Rubus occidentalis L.) has been limited by a lack of genetic diversity in elite germplasm. Black raspberry cultivars have been noted for showing very few phenotypic differences and seedlings from crosses between cultivars for a lack of segregation for important ...

Molecular genetics research in ADHD: ethical considerations concerning patients' benefit and resource allocation.

PubMed

Rothenberger, Lillian Geza

2012-12-01

Immense resource allocations have led to great data output in genetic research. Concerning ADHD resources spent on genetic research are less than those spent on clinical research. But there are successful efforts made to increase support for molecular genetics research in ADHD. Concerning genetics no evidence based conclusive results have significant impact on prevention, diagnosis or treatment yet. With regard to ethical aspects like the patients' benefit and limited resources the question arises if it is indicated to think about a new balance of resource allocation between molecular genetics and non-genetics research in ADHD. An ethical reflection was performed focusing on recent genetic studies and reviews based on a selective literature search. There are plausible reasons why genetic research results in ADHD are somehow disappointing for clinical practice so far. Researchers try to overcome these gaps systematically, without knowing what the potential future benefits for the patients might be. Non-genetic diagnostic/therapeutic research may lead to clinically relevant findings within a shorter period of time. On the other hand, non-genetic research in ADHD may be nurtured by genetic approaches. But, with the latter there exist significant risks of harm like stigmatization and concerns regarding data protection. Isolated speeding up resources of genetic research in ADHD seems questionable from an ethical point of view. There is a need to find a new balance of resource allocation between genetic and non-genetic research in ADHD, probably by integrating genetics more systematically into clinical research. A transdisciplinary debate is recommended. Copyright © 2012 Wiley Periodicals, Inc.

Recommendations for developing and applying genetic tools to assess and manage biological invasions in marine ecosystems

PubMed Central

Darling, John A.; Galil, Bella S.; Carvalho, Gary R.; Rius, Marc; Viard, Frédérique; Piraino, Stefano

2018-01-01

The European Union’s Marine Strategy Framework Directive (MSFD) aims to adopt integrated ecosystem management approaches to achieve or maintain “Good Environmental Status” for marine waters, habitats and resources, including mitigation of the negative effects of non-indigenous species (NIS). The Directive further seeks to promote broadly standardized monitoring efforts and assessment of temporal trends in marine ecosystem condition, incorporating metrics describing the distribution and impacts of NIS. Accomplishing these goals will require application of advanced tools for NIS surveillance and risk assessment, particularly given known challenges associated with surveying and monitoring with traditional methods. In the past decade, a host of methods based on nucleic acids (DNA and RNA) analysis have been developed or advanced that promise to dramatically enhance capacity in assessing and managing NIS. However, ensuring that these rapidly evolving approaches remain accessible and responsive to the needs of resource managers remains a challenge. This paper provides recommendations for future development of these genetic tools for assessment and management of NIS in marine systems, within the context of the explicit requirements of the MSFD. Issues considered include technological innovation, methodological standardization, data sharing and collaboration, and the critical importance of shared foundational resources, particularly integrated taxonomic expertise. Though the recommendations offered here are not exhaustive, they provide a basis for future intentional (and international) collaborative development of a genetic toolkit for NIS research, capable of fulfilling the immediate and long term goals of marine ecosystem and resource conservation. PMID:29681680

Genetic diversity and differentiation of exotic and American commercial cattle breeds raised in Brazil.

PubMed

Brasil, B S A F; Coelho, E G A; Drummond, M G; Oliveira, D A A

2013-11-18

The Brazilian cattle population is mainly composed of breeds of zebuine origin and their American derivatives. Comprehensive knowledge about the genetic diversity of these populations is fundamental for animal breeding programs and the conservation of genetic resources. This study aimed to assess the phylogenetic relationships, levels of genetic diversity, and patterns of taurine/zebuine admixture among 9 commercial cattle breeds raised in Brazil. Analysis of DNA polymorphisms was performed on 2965 animals using the 11 microsatellite markers recommended by the International Society of Animal Genetics. High genetic diversity was detected in all breeds, even though significant inbreeding was observed within some. Differences among the breeds accounted for 14.72% of the total genetic variability, and genetic differentiation was higher among taurine than among zebuine cattle. Of note, Nelore cattle presented with high levels of admixture, which is consistent with the history of frequent gene flow during the establishment of this breed in Brazil. Furthermore, significant genetic variability was partitioned within the commercial cattle breeds formed in America, which, therefore, comprise important resources of genetic diversity in the tropics. The genetic characterization of these important Brazilian breeds may now facilitate the development of management and breeding programs for these populations.

National Newborn Screening and Genetics Resource Center

MedlinePlus

... GENERAL INFORMATION Conditions Screened by US Programs General Resources Genetics Birth Defects Hearing Screening FOR PROFESSIONALS ACT Sheets(ACMG) General Resources Newborn Screening Genetics Birth Defects FOR FAMILIES FAQs ...

Provision of genetics services on Guam.

PubMed

McWalter, Kirsty; Hasegawa, Lianne; Au, Sylvia Mann

2013-12-01

Guam's geographic isolation and lack of community resources have resulted in unique healthcare needs. In 2006, the Western States Genetic Services Collaborative (WSGSC) conducted a genetics needs assessment and found that professional development is limited, families lack access to genetic services, and improved coverage of genetic testing is needed. With funding from the WSGSC, a Guam genetics outreach clinic was established and staffed by genetic counselors and a medical geneticist from Hawaii. Four clinics have been held to date. Although several challenges have been encountered, including minimal coverage of genetic testing by Guam insurance companies, limited referrals for families with private insurance, and inappropriate referral indications, the outreach clinic has been successful at increasing access to genetic services and improving professional development. With more collaborative work by staff from Guam, Hawaii, and the WSGSC, provision and reimbursement of genetic services and testing will continue to improve.

Genome resources for climate-resilient cowpea, an essential crop for food security.

PubMed

Muñoz-Amatriaín, María; Mirebrahim, Hamid; Xu, Pei; Wanamaker, Steve I; Luo, MingCheng; Alhakami, Hind; Alpert, Matthew; Atokple, Ibrahim; Batieno, Benoit J; Boukar, Ousmane; Bozdag, Serdar; Cisse, Ndiaga; Drabo, Issa; Ehlers, Jeffrey D; Farmer, Andrew; Fatokun, Christian; Gu, Yong Q; Guo, Yi-Ning; Huynh, Bao-Lam; Jackson, Scott A; Kusi, Francis; Lawley, Cynthia T; Lucas, Mitchell R; Ma, Yaqin; Timko, Michael P; Wu, Jiajie; You, Frank; Barkley, Noelle A; Roberts, Philip A; Lonardi, Stefano; Close, Timothy J

2017-03-01

Cowpea (Vigna unguiculata L. Walp.) is a legume crop that is resilient to hot and drought-prone climates, and a primary source of protein in sub-Saharan Africa and other parts of the developing world. However, genome resources for cowpea have lagged behind most other major crops. Here we describe foundational genome resources and their application to the analysis of germplasm currently in use in West African breeding programs. Resources developed from the African cultivar IT97K-499-35 include a whole-genome shotgun (WGS) assembly, a bacterial artificial chromosome (BAC) physical map, and assembled sequences from 4355 BACs. These resources and WGS sequences of an additional 36 diverse cowpea accessions supported the development of a genotyping assay for 51 128 SNPs, which was then applied to five bi-parental RIL populations to produce a consensus genetic map containing 37 372 SNPs. This genetic map enabled the anchoring of 100 Mb of WGS and 420 Mb of BAC sequences, an exploration of genetic diversity along each linkage group, and clarification of macrosynteny between cowpea and common bean. The SNP assay enabled a diversity analysis of materials from West African breeding programs. Two major subpopulations exist within those materials, one of which has significant parentage from South and East Africa and more diversity. There are genomic regions of high differentiation between subpopulations, one of which coincides with a cluster of nodulin genes. The new resources and knowledge help to define goals and accelerate the breeding of improved varieties to address food security issues related to limited-input small-holder farming and climate stress. © 2016 The Authors. The Plant Journal published by John Wiley & Sons Ltd and Society for Experimental Biology.

Panmictic and Clonal Evolution on a Single Patchy Resource Produces Polymorphic Foraging Guilds

PubMed Central

Getz, Wayne M.; Salter, Richard; Lyons, Andrew J.; Sippl-Swezey, Nicolas

2015-01-01

We develop a stochastic, agent-based model to study how genetic traits and experiential changes in the state of agents and available resources influence individuals’ foraging and movement behaviors. These behaviors are manifest as decisions on when to stay and exploit a current resource patch or move to a particular neighboring patch, based on information of the resource qualities of the patches and the anticipated level of intraspecific competition within patches. We use a genetic algorithm approach and an individual’s biomass as a fitness surrogate to explore the foraging strategy diversity of evolving guilds under clonal versus hermaphroditic sexual reproduction. We first present the resource exploitation processes, movement on cellular arrays, and genetic algorithm components of the model. We then discuss their implementation on the Nova software platform. This platform seamlessly combines the dynamical systems modeling of consumer-resource interactions with agent-based modeling of individuals moving over a landscapes, using an architecture that lays transparent the following four hierarchical simulation levels: 1.) within-patch consumer-resource dynamics, 2.) within-generation movement and competition mitigation processes, 3.) across-generation evolutionary processes, and 4.) multiple runs to generate the statistics needed for comparative analyses. The focus of our analysis is on the question of how the biomass production efficiency and the diversity of guilds of foraging strategy types, exploiting resources over a patchy landscape, evolve under clonal versus random hermaphroditic sexual reproduction. Our results indicate greater biomass production efficiency under clonal reproduction only at higher population densities, and demonstrate that polymorphisms evolve and are maintained under random mating systems. The latter result questions the notion that some type of associative mating structure is needed to maintain genetic polymorphisms among individuals exploiting a common patchy resource on an otherwise spatially homogeneous landscape. PMID:26274613

Redesigning the exploitation of wheat genetic resources.

PubMed

Longin, C Friedrich H; Reif, Jochen C

2014-10-01

More than half a million wheat genetic resources are resting in gene banks worldwide. Unlocking their hidden favorable genetic diversity for breeding is pivotal for enhancing grain yield potential, and averting future food shortages. Here, we propose exploiting recent advances in hybrid wheat technology to uncover the masked breeding values of wheat genetic resources. The gathered phenotypic information will enable a targeted choice of accessions with high value for pre-breeding among this plethora of genetic resources. We intend to provoke a paradigm shift in pre-breeding strategies for grain yield, moving away from allele mining toward genome-wide selection to bridge the yield gap between genetic resources and elite breeding pools. Copyright © 2014 Elsevier Ltd. All rights reserved.

The Human Proteome Project: Unlocking the Mysteries of Human Life and Unleashing Its Potential

DTIC Science & Technology

2011-02-16

Australasian Genetics Resource Book. June 2007. Accessed September 27, 2010. www.genetics.com.au/pdf/factsheets/fs24.pdf. 2 White House, Office of...Project and Beyond." The Australasian Genetics Resource Book. June 2007. Accessed September 27, 2010. www.genetics.com.au/pdf/factsheets/fs24.pdf...9 Centre for Genetics Education. "The Human Genetic Code – The Human Genome Project and Beyond." The Australasian Genetics Resource Book. June

GGDonto ontology as a knowledge-base for genetic diseases and disorders of glycan metabolism and their causative genes.

PubMed

Solovieva, Elena; Shikanai, Toshihide; Fujita, Noriaki; Narimatsu, Hisashi

2018-04-18

Inherited mutations in glyco-related genes can affect the biosynthesis and degradation of glycans and result in severe genetic diseases and disorders. The Glyco-Disease Genes Database (GDGDB), which provides information about these diseases and disorders as well as their causative genes, has been developed by the Research Center for Medical Glycoscience (RCMG) and released in April 2010. GDGDB currently provides information on about 80 genetic diseases and disorders caused by single-gene mutations in glyco-related genes. Many biomedical resources provide information about genetic disorders and genes involved in their pathogenesis, but resources focused on genetic disorders known to be related to glycan metabolism are lacking. With the aim of providing more comprehensive knowledge on genetic diseases and disorders of glycan biosynthesis and degradation, we enriched the content of the GDGDB database and improved the methods for data representation. We developed the Genetic Glyco-Diseases Ontology (GGDonto) and a RDF/SPARQL-based user interface using Semantic Web technologies. In particular, we represented the GGDonto content using Semantic Web languages, such as RDF, RDFS, SKOS, and OWL, and created an interactive user interface based on SPARQL queries. This user interface provides features to browse the hierarchy of the ontology, view detailed information on diseases and related genes, and find relevant background information. Moreover, it provides the ability to filter and search information by faceted and keyword searches. Focused on the molecular etiology, pathogenesis, and clinical manifestations of genetic diseases and disorders of glycan metabolism and developed as a knowledge-base for this scientific field, GGDonto provides comprehensive information on various topics, including links to aid the integration with other scientific resources. The availability and accessibility of this knowledge will help users better understand how genetic defects impact the metabolism of glycans as well as how this impaired metabolism affects various biological functions and human health. In this way, GGDonto will be useful in fields related to glycoscience, including cell biology, biotechnology, and biomedical, and pharmaceutical research.

A first genetic map of date palm (Phoenix dactylifera) reveals long-range genome structure conservation in the palms

PubMed Central

2014-01-01

Background The date palm is one of the oldest cultivated fruit trees. It is critical in many ways to cultures in arid lands by providing highly nutritious fruit while surviving extreme heat and environmental conditions. Despite its importance from antiquity, few genetic resources are available for improving the productivity and development of the dioecious date palm. To date there has been no genetic map and no sex chromosome has been identified. Results Here we present the first genetic map for date palm and identify the putative date palm sex chromosome. We placed ~4000 markers on the map using nearly 1200 framework markers spanning a total of 1293 cM. We have integrated the genetic map, derived from the Khalas cultivar, with the draft genome and placed up to 19% of the draft genome sequence scaffolds onto linkage groups for the first time. This analysis revealed approximately ~1.9 cM/Mb on the map. Comparison of the date palm linkage groups revealed significant long-range synteny to oil palm. Analysis of the date palm sex-determination region suggests it is telomeric on linkage group 12 and recombination is not suppressed in the full chromosome. Conclusions Based on a modified gentoyping-by-sequencing approach we have overcome challenges due to lack of genetic resources and provide the first genetic map for date palm. Combined with the recent draft genome sequence of the same cultivar, this resource offers a critical new tool for date palm biotechnology, palm comparative genomics and a better understanding of sex chromosome development in the palms. PMID:24735434

Transcriptome sequencing for high throughput SNP development and genetic mapping in Pea

PubMed Central

2014-01-01

Background Pea has a complex genome of 4.3 Gb for which only limited genomic resources are available to date. Although SNP markers are now highly valuable for research and modern breeding, only a few are described and used in pea for genetic diversity and linkage analysis. Results We developed a large resource by cDNA sequencing of 8 genotypes representative of modern breeding material using the Roche 454 technology, combining both long reads (400 bp) and high coverage (3.8 million reads, reaching a total of 1,369 megabases). Sequencing data were assembled and generated a 68 K unigene set, from which 41 K were annotated from their best blast hit against the model species Medicago truncatula. Annotated contigs showed an even distribution along M. truncatula pseudochromosomes, suggesting a good representation of the pea genome. 10 K pea contigs were found to be polymorphic among the genetic material surveyed, corresponding to 35 K SNPs. We validated a subset of 1538 SNPs through the GoldenGate assay, proving their ability to structure a diversity panel of breeding germplasm. Among them, 1340 were genetically mapped and used to build a new consensus map comprising a total of 2070 markers. Based on blast analysis, we could establish 1252 bridges between our pea consensus map and the pseudochromosomes of M. truncatula, which provides new insight on synteny between the two species. Conclusions Our approach created significant new resources in pea, i.e. the most comprehensive genetic map to date tightly linked to the model species M. truncatula and a large SNP resource for both academic research and breeding. PMID:24521263

Development of novel genic microsatellite markers from transcriptome sequencing in sugar maple (Acer saccharum Marsh.).

PubMed

Harmon, Monica; Lane, Thomas; Staton, Margaret; Coggeshall, Mark V; Best, Teodora; Chen, Chien-Chih; Liang, Haiying; Zembower, Nicole; Drautz-Moses, Daniela I; Hwee, Yap Zhei; Schuster, Stephan C; Schlarbaum, Scott E; Carlson, John E; Gailing, Oliver

2017-08-08

Sugar maple (Acer saccharum Marsh.) is a hardwood tree species native to northeastern North America and economically valued for its wood and sap. Yet, few molecular genetic resources have been developed for this species to date. Microsatellite markers have been a useful tool in population genetics, e.g., to monitor genetic variation and to analyze gene flow patterns. The objective of this study is to develop a reference transcriptome and microsatellite markers in sugar maple. A set of 117,861 putative unique transcripts were assembled using 29.2 Gb of RNA sequencing data derived from different tissues and stress treatments. From this set of sequences a total of 1068 microsatellite motifs were identified. Out of 58 genic microsatellite markers tested on a population of 47 sugar maple trees in upper Michigan, 22 amplified well, of which 16 were polymorphic and 6 were monomorphic. Values for expected heterozygosity varied from 0.224 to 0.726 for individual loci. Of the 16 polymorphic markers, 15 exhibited transferability to other Acer L. species. Genic microsatellite markers can be applied to analyze genetic variation in potentially adaptive genes relative to genomic reference markers as a basis for the management of sugar maple genetic resources in the face of climate change.

An improved 10-SSR pyrus fingerprinting DNA test to confirm parentage [abstract

USDA-ARS?s Scientific Manuscript database

Pedigree confirmation is a critical part of breeding, managing genetic resources, and developing genetic mapping populations for out-crossing plants, such as the genus Pyrus. Individuals which are not progeny of a biparental cross can cause mapping errors or result in the costly genotyping of indivi...

USDA forest service southern region – It’s all about GRITS

Treesearch

Barbara S. Crane; Kevin M. Potter

2017-01-01

Genetic resource management programs across the U.S. Department of Agriculture Forest Service (USDA FS) play a key role in supporting successful land management activities. The programs are responsible for developing and providing plant material for revegetation, seed management guidelines, emergency fire recovery assistance, genetic conservation strategies, climate...

Inseminating fresh or cryopreserved semen for maximum efficiency: implications for gene banks and industry

USDA-ARS?s Scientific Manuscript database

Developing germplasm collections in gene banks for animal genetic resources requires establishing germplasm collection goals, that consider capturing the genetic diversity of the population in question and the amount of germplasm required for reconstitution of the population or for other purposes. C...

Building a model: developing genomic resources for common milkweed (Asclepias syriaca) with low coverage genome sequencing

PubMed Central

2011-01-01

Background Milkweeds (Asclepias L.) have been extensively investigated in diverse areas of evolutionary biology and ecology; however, there are few genetic resources available to facilitate and compliment these studies. This study explored how low coverage genome sequencing of the common milkweed (Asclepias syriaca L.) could be useful in characterizing the genome of a plant without prior genomic information and for development of genomic resources as a step toward further developing A. syriaca as a model in ecology and evolution. Results A 0.5× genome of A. syriaca was produced using Illumina sequencing. A virtually complete chloroplast genome of 158,598 bp was assembled, revealing few repeats and loss of three genes: accD, clpP, and ycf1. A nearly complete rDNA cistron (18S-5.8S-26S; 7,541 bp) and 5S rDNA (120 bp) sequence were obtained. Assessment of polymorphism revealed that the rDNA cistron and 5S rDNA had 0.3% and 26.7% polymorphic sites, respectively. A partial mitochondrial genome sequence (130,764 bp), with identical gene content to tobacco, was also assembled. An initial characterization of repeat content indicated that Ty1/copia-like retroelements are the most common repeat type in the milkweed genome. At least one A. syriaca microread hit 88% of Catharanthus roseus (Apocynaceae) unigenes (median coverage of 0.29×) and 66% of single copy orthologs (COSII) in asterids (median coverage of 0.14×). From this partial characterization of the A. syriaca genome, markers for population genetics (microsatellites) and phylogenetics (low-copy nuclear genes) studies were developed. Conclusions The results highlight the promise of next generation sequencing for development of genomic resources for any organism. Low coverage genome sequencing allows characterization of the high copy fraction of the genome and exploration of the low copy fraction of the genome, which facilitate the development of molecular tools for further study of a target species and its relatives. This study represents a first step in the development of a community resource for further study of plant-insect co-evolution, anti-herbivore defense, floral developmental genetics, reproductive biology, chemical evolution, population genetics, and comparative genomics using milkweeds, and A. syriaca in particular, as ecological and evolutionary models. PMID:21542930

Building a model: developing genomic resources for common milkweed (Asclepias syriaca) with low coverage genome sequencing.

PubMed

Straub, Shannon C K; Fishbein, Mark; Livshultz, Tatyana; Foster, Zachary; Parks, Matthew; Weitemier, Kevin; Cronn, Richard C; Liston, Aaron

2011-05-04

Milkweeds (Asclepias L.) have been extensively investigated in diverse areas of evolutionary biology and ecology; however, there are few genetic resources available to facilitate and compliment these studies. This study explored how low coverage genome sequencing of the common milkweed (Asclepias syriaca L.) could be useful in characterizing the genome of a plant without prior genomic information and for development of genomic resources as a step toward further developing A. syriaca as a model in ecology and evolution. A 0.5× genome of A. syriaca was produced using Illumina sequencing. A virtually complete chloroplast genome of 158,598 bp was assembled, revealing few repeats and loss of three genes: accD, clpP, and ycf1. A nearly complete rDNA cistron (18S-5.8S-26S; 7,541 bp) and 5S rDNA (120 bp) sequence were obtained. Assessment of polymorphism revealed that the rDNA cistron and 5S rDNA had 0.3% and 26.7% polymorphic sites, respectively. A partial mitochondrial genome sequence (130,764 bp), with identical gene content to tobacco, was also assembled. An initial characterization of repeat content indicated that Ty1/copia-like retroelements are the most common repeat type in the milkweed genome. At least one A. syriaca microread hit 88% of Catharanthus roseus (Apocynaceae) unigenes (median coverage of 0.29×) and 66% of single copy orthologs (COSII) in asterids (median coverage of 0.14×). From this partial characterization of the A. syriaca genome, markers for population genetics (microsatellites) and phylogenetics (low-copy nuclear genes) studies were developed. The results highlight the promise of next generation sequencing for development of genomic resources for any organism. Low coverage genome sequencing allows characterization of the high copy fraction of the genome and exploration of the low copy fraction of the genome, which facilitate the development of molecular tools for further study of a target species and its relatives. This study represents a first step in the development of a community resource for further study of plant-insect co-evolution, anti-herbivore defense, floral developmental genetics, reproductive biology, chemical evolution, population genetics, and comparative genomics using milkweeds, and A. syriaca in particular, as ecological and evolutionary models.

Understanding genetics: a primer for occupational health practice.

PubMed

Wright, Lynette

2005-12-01

Because biologic diversity is essential for life, genes have developed many versions that may be further modified by interaction with other genes and with environmental factors. Polymorphic alterations of genetic material influence drug responses, predisposition or resistance to disease, and susceptibility to environmental toxicity. The occupational health professional should be aware of rapidly changing genetic tests, be able to distinguish between screening and diagnostic modalities, be able to access genetic resources to find the latest protocols, and should consider the ethical, legal, and social implications of genetic testing in the workplace.

The Emerging Oilseed Crop Sesamum indicum Enters the “Omics” Era

PubMed Central

Dossa, Komivi; Diouf, Diaga; Wang, Linhai; Wei, Xin; Zhang, Yanxin; Niang, Mareme; Fonceka, Daniel; Yu, Jingyin; Mmadi, Marie A.; Yehouessi, Louis W.; Liao, Boshou; Zhang, Xiurong; Cisse, Ndiaga

2017-01-01

Sesame (Sesamum indicum L.) is one of the oldest oilseed crops widely grown in Africa and Asia for its high-quality nutritional seeds. It is well adapted to harsh environments and constitutes an alternative cash crop for smallholders in developing countries. Despite its economic and nutritional importance, sesame is considered as an orphan crop because it has received very little attention from science. As a consequence, it lags behind the other major oil crops as far as genetic improvement is concerned. In recent years, the scenario has considerably changed with the decoding of the sesame nuclear genome leading to the development of various genomic resources including molecular markers, comprehensive genetic maps, high-quality transcriptome assemblies, web-based functional databases and diverse daft genome sequences. The availability of these tools in association with the discovery of candidate genes and quantitative trait locis for key agronomic traits including high oil content and quality, waterlogging and drought tolerance, disease resistance, cytoplasmic male sterility, high yield, pave the way to the development of some new strategies for sesame genetic improvement. As a result, sesame has graduated from an “orphan crop” to a “genomic resource-rich crop.” With the limited research teams working on sesame worldwide, more synergic efforts are needed to integrate these resources in sesame breeding for productivity upsurge, ensuring food security and improved livelihood in developing countries. This review retraces the evolution of sesame research by highlighting the recent advances in the “Omics” area and also critically discusses the future prospects for a further genetic improvement and a better expansion of this crop. PMID:28713412

The Emerging Oilseed Crop Sesamum indicum Enters the "Omics" Era.

PubMed

Dossa, Komivi; Diouf, Diaga; Wang, Linhai; Wei, Xin; Zhang, Yanxin; Niang, Mareme; Fonceka, Daniel; Yu, Jingyin; Mmadi, Marie A; Yehouessi, Louis W; Liao, Boshou; Zhang, Xiurong; Cisse, Ndiaga

2017-01-01

Sesame ( Sesamum indicum L.) is one of the oldest oilseed crops widely grown in Africa and Asia for its high-quality nutritional seeds. It is well adapted to harsh environments and constitutes an alternative cash crop for smallholders in developing countries. Despite its economic and nutritional importance, sesame is considered as an orphan crop because it has received very little attention from science. As a consequence, it lags behind the other major oil crops as far as genetic improvement is concerned. In recent years, the scenario has considerably changed with the decoding of the sesame nuclear genome leading to the development of various genomic resources including molecular markers, comprehensive genetic maps, high-quality transcriptome assemblies, web-based functional databases and diverse daft genome sequences. The availability of these tools in association with the discovery of candidate genes and quantitative trait locis for key agronomic traits including high oil content and quality, waterlogging and drought tolerance, disease resistance, cytoplasmic male sterility, high yield, pave the way to the development of some new strategies for sesame genetic improvement. As a result, sesame has graduated from an "orphan crop" to a "genomic resource-rich crop." With the limited research teams working on sesame worldwide, more synergic efforts are needed to integrate these resources in sesame breeding for productivity upsurge, ensuring food security and improved livelihood in developing countries. This review retraces the evolution of sesame research by highlighting the recent advances in the "Omics" area and also critically discusses the future prospects for a further genetic improvement and a better expansion of this crop.

MGIS: managing banana (Musa spp.) genetic resources information and high-throughput genotyping data

PubMed Central

Guignon, V.; Sempere, G.; Sardos, J.; Hueber, Y.; Duvergey, H.; Andrieu, A.; Chase, R.; Jenny, C.; Hazekamp, T.; Irish, B.; Jelali, K.; Adeka, J.; Ayala-Silva, T.; Chao, C.P.; Daniells, J.; Dowiya, B.; Effa effa, B.; Gueco, L.; Herradura, L.; Ibobondji, L.; Kempenaers, E.; Kilangi, J.; Muhangi, S.; Ngo Xuan, P.; Paofa, J.; Pavis, C.; Thiemele, D.; Tossou, C.; Sandoval, J.; Sutanto, A.; Vangu Paka, G.; Yi, G.; Van den houwe, I.; Roux, N.

2017-01-01

Abstract Unraveling the genetic diversity held in genebanks on a large scale is underway, due to advances in Next-generation sequence (NGS) based technologies that produce high-density genetic markers for a large number of samples at low cost. Genebank users should be in a position to identify and select germplasm from the global genepool based on a combination of passport, genotypic and phenotypic data. To facilitate this, a new generation of information systems is being designed to efficiently handle data and link it with other external resources such as genome or breeding databases. The Musa Germplasm Information System (MGIS), the database for global ex situ-held banana genetic resources, has been developed to address those needs in a user-friendly way. In developing MGIS, we selected a generic database schema (Chado), the robust content management system Drupal for the user interface, and Tripal, a set of Drupal modules which links the Chado schema to Drupal. MGIS allows germplasm collection examination, accession browsing, advanced search functions, and germplasm orders. Additionally, we developed unique graphical interfaces to compare accessions and to explore them based on their taxonomic information. Accession-based data has been enriched with publications, genotyping studies and associated genotyping datasets reporting on germplasm use. Finally, an interoperability layer has been implemented to facilitate the link with complementary databases like the Banana Genome Hub and the MusaBase breeding database. Database URL: https://www.crop-diversity.org/mgis/ PMID:29220435

Career Education Resource Guide for Biology. Working Draft.

ERIC Educational Resources Information Center

Louisiana State Dept. of Education, Baton Rouge.

The resource guide integrates learning activities in biological science with an exploration of careers in biology or related fields. The materials are divided into seven units: tools of the scientist, basis for life, diversity (protists, plants, animals), structure and function, continuity (reproduction, development, and genetics), evolution, and…

Introduction to the newly released GRIN-Global

USDA-ARS?s Scientific Manuscript database

The Germplasm Resources Information Network (GRIN) is an information management system that curates data for the USDA-ARS genetic resource collections. GRIN was developed in the late 1980s and has been incrementally improved over the past 35 years. A major revision was recently deployed to service t...

Eugenics and Mandatory Informed Prenatal Genetic Testing: A Unique Perspective from China.

PubMed

Zhang, Di; Ng, Vincent H; Wang, Zhaochen; Zhai, Xiaomei; Lie, Reidar K

2016-08-01

The application of genetic technologies in China, especially in the area of prenatal genetic testing, is rapidly increasing in China. In the wealthy regions of China, prenatal genetic testing is already very widely adopted. We argue that the government should actively promote prenatal genetic testing to the poor areas of the country. In fact, the government should prioritize resources first to make prenatal genetic testing a standard routine care with an opt-out model in these area. Healthcare professions would be required to inform pregnant women about the availability of genetic testing and provide free testing on a routine basis unless the parents choose not to do so. We argue that this proposal will allow parents to make a more informed decision about their reproductive choices. Secondarily, this proposal will attract more healthcare professionals and other healthcare resources to improve the healthcare infrastructures in the less-developed regions of the country. This will help to reduce the inequity of accessing healthcare services between in different regions of China. We further argue that this policy proposal is not practicing eugenics. © 2015 John Wiley & Sons Ltd.

Characterization of genome-wide microsatellite markers in rabbitfishes, an important resource for artisanal fisheries in the Indo-West Pacific.

PubMed

Kiper, Ilkser Erdem; Bloomer, Paulette; Borsa, Philippe; Hoareau, Thierry Bernard

2018-02-01

Rabbitfishes are reef-associated fishes that support local fisheries throughout the Indo-West Pacific region. Sound management of the resource requires the development of molecular tools for appropriate stock delimitation of the different species in the family. Microsatellite markers were developed for the cordonnier, Siganus sutor, and their potential for cross-amplification was investigated in 12 congeneric species. A library of 792 repeat-containing sequences was built. Nineteen sets of newly developed primers, and 14 universal finfish microsatellites were tested in S. sutor. Amplification success of the 19 Siganus-specific markers ranged from 32 to 79% in the 12 other Siganus species, slightly decreasing when the genetic distance of the target species to S. sutor increased. Seventeen of these markers were polymorphic in S. sutor and were further assayed in S. luridus, S. rivulatus, and S. spinus, of which respectively 9, 10 and 8 were polymorphic. Statistical power analysis and an analysis of molecular variance showed that subtle genetic differentiation can be detected using these markers, highlighting their utility for the study of genetic diversity and population genetic structure in rabbitfishes.

DT2008: A Promising New Genetic Resource for Improved Drought Tolerance in Soybean When Solely Dependent on Symbiotic N2 Fixation

PubMed Central

Sulieman, Saad; Ha, Chien Van; Nasr Esfahani, Maryam; Watanabe, Yasuko; Nishiyama, Rie; Pham, Chung Thi Bao; Nguyen, Dong Van; Tran, Lam-Son Phan

2015-01-01

Water deficit is one of the major constraints for soybean production in Vietnam. The soybean breeding research efforts conducted at the Agriculture Genetics Institute (AGI) of Vietnam resulted in the development of promising soybean genotypes, suitable for the drought-stressed areas in Vietnam and other countries. Such a variety, namely, DT2008, was recommended by AGI and widely used throughout the country. The aim of this work was to assess the growth of shoots, roots, and nodules of DT2008 versus Williams 82 (W82) in response to drought and subsequent rehydration in symbiotic association as a means to provide genetic resources for genomic research. Better shoot, root, and nodule growth and development were observed in the cultivar DT2008 under sufficient, water deficit, and recovery conditions. Our results represent a good foundation for further comparison of DT2008 and W82 at molecular levels using high throughput omic technologies, which will provide huge amounts of data, enabling us to understand the genetic network involved in regulation of soybean responses to water deficit and increasing the chances of developing drought-tolerant cultivars. PMID:25685802

Isozymes and the genetic resources of forest trees

Treesearch

A. H. D. Brown; G. F. Moran

1981-01-01

Genetic data are an essential prerequisite for analysing the genetic structure of tree populations. The isozyme technique is the best currently available method for obtaining such data. Despite several shortcomings, isozyme data directly evaluate the genetic resources of forest trees, and can thus be used to monitor and manipulate these resources. For example,...

Biotechnologies for the management of genetic resources for food and agriculture.

PubMed

Lidder, Preetmoninder; Sonnino, Andrea

2012-01-01

In recent years, the land area under agriculture has declined as also has the rate of growth in agricultural productivity while the demand for food continues to escalate. The world population now stands at 7 billion and is expected to reach 9 billion in 2045. A broad range of agricultural genetic diversity needs to be available and utilized in order to feed this growing population. Climate change is an added threat to biodiversity that will significantly impact genetic resources for food and agriculture (GRFA) and food production. There is no simple, all-encompassing solution to the challenges of increasing productivity while conserving genetic diversity. Sustainable management of GRFA requires a multipronged approach, and as outlined in the paper, biotechnologies can provide powerful tools for the management of GRFA. These tools vary in complexity from those that are relatively simple to those that are more sophisticated. Further, advances in biotechnologies are occurring at a rapid pace and provide novel opportunities for more effective and efficient management of GRFA. Biotechnology applications must be integrated with ongoing conventional breeding and development programs in order to succeed. Additionally, the generation, adaptation, and adoption of biotechnologies require a consistent level of financial and human resources and appropriate policies need to be in place. These issues were also recognized by Member States at the FAO international technical conference on Agricultural Biotechnologies for Developing Countries (ABDC-10), which took place in March 2010 in Mexico. At the end of the conference, the Member States reached a number of key conclusions, agreeing, inter alia, that developing countries should significantly increase sustained investments in capacity building and the development and use of biotechnologies to maintain the natural resource base; that effective and enabling national biotechnology policies and science-based regulatory frameworks can facilitate the development and appropriate use of biotechnologies in developing countries; and that FAO and other relevant international organizations and donors should significantly increase their efforts to support the strengthening of national capacities in the development and appropriate use of pro-poor agricultural biotechnologies. Copyright © 2012 Elsevier Inc. All rights reserved.

Potential International Approaches to Ownership/Control of Human Genetic Resources.

PubMed

Rhodes, Catherine

2016-09-01

In its governance activities for genetic resources, the international community has adopted various approaches to their ownership, including: free access; common heritage of mankind; intellectual property rights; and state sovereign rights. They have also created systems which combine elements of these approaches. While governance of plant and animal genetic resources is well-established internationally, there has not yet been a clear approach selected for human genetic resources. Based on assessment of the goals which international governance of human genetic resources ought to serve, and the implications for how they will be accessed and utilised, it is argued that common heritage of mankind will be the most appropriate approach to adopt to their ownership/control. It does this with the aim of stimulating discussion in this area and providing a starting point for deeper consideration of how a common heritage of mankind, or similar, regime for human genetic resources would function and be implemented.

Multi-level, multi-scale resource selection functions and resistance surfaces for conservation planning: Pumas as a case study

PubMed Central

Vickers, T. Winston; Ernest, Holly B.; Boyce, Walter M.

2017-01-01

The importance of examining multiple hierarchical levels when modeling resource use for wildlife has been acknowledged for decades. Multi-level resource selection functions have recently been promoted as a method to synthesize resource use across nested organizational levels into a single predictive surface. Analyzing multiple scales of selection within each hierarchical level further strengthens multi-level resource selection functions. We extend this multi-level, multi-scale framework to modeling resistance for wildlife by combining multi-scale resistance surfaces from two data types, genetic and movement. Resistance estimation has typically been conducted with one of these data types, or compared between the two. However, we contend it is not an either/or issue and that resistance may be better-modeled using a combination of resistance surfaces that represent processes at different hierarchical levels. Resistance surfaces estimated from genetic data characterize temporally broad-scale dispersal and successful breeding over generations, whereas resistance surfaces estimated from movement data represent fine-scale travel and contextualized movement decisions. We used telemetry and genetic data from a long-term study on pumas (Puma concolor) in a highly developed landscape in southern California to develop a multi-level, multi-scale resource selection function and a multi-level, multi-scale resistance surface. We used these multi-level, multi-scale surfaces to identify resource use patches and resistant kernel corridors. Across levels, we found puma avoided urban, agricultural areas, and roads and preferred riparian areas and more rugged terrain. For other landscape features, selection differed among levels, as did the scales of selection for each feature. With these results, we developed a conservation plan for one of the most isolated puma populations in the U.S. Our approach captured a wide spectrum of ecological relationships for a population, resulted in effective conservation planning, and can be readily applied to other wildlife species. PMID:28609466

Multi-level, multi-scale resource selection functions and resistance surfaces for conservation planning: Pumas as a case study.

PubMed

Zeller, Katherine A; Vickers, T Winston; Ernest, Holly B; Boyce, Walter M

2017-01-01

The importance of examining multiple hierarchical levels when modeling resource use for wildlife has been acknowledged for decades. Multi-level resource selection functions have recently been promoted as a method to synthesize resource use across nested organizational levels into a single predictive surface. Analyzing multiple scales of selection within each hierarchical level further strengthens multi-level resource selection functions. We extend this multi-level, multi-scale framework to modeling resistance for wildlife by combining multi-scale resistance surfaces from two data types, genetic and movement. Resistance estimation has typically been conducted with one of these data types, or compared between the two. However, we contend it is not an either/or issue and that resistance may be better-modeled using a combination of resistance surfaces that represent processes at different hierarchical levels. Resistance surfaces estimated from genetic data characterize temporally broad-scale dispersal and successful breeding over generations, whereas resistance surfaces estimated from movement data represent fine-scale travel and contextualized movement decisions. We used telemetry and genetic data from a long-term study on pumas (Puma concolor) in a highly developed landscape in southern California to develop a multi-level, multi-scale resource selection function and a multi-level, multi-scale resistance surface. We used these multi-level, multi-scale surfaces to identify resource use patches and resistant kernel corridors. Across levels, we found puma avoided urban, agricultural areas, and roads and preferred riparian areas and more rugged terrain. For other landscape features, selection differed among levels, as did the scales of selection for each feature. With these results, we developed a conservation plan for one of the most isolated puma populations in the U.S. Our approach captured a wide spectrum of ecological relationships for a population, resulted in effective conservation planning, and can be readily applied to other wildlife species.

GRIN-Global: An International Project to Develop a Global Plant Genebank and Information Management System

USDA-ARS?s Scientific Manuscript database

Many of the world's national genebanks, responsible for the safeguarding and availability of their country's Plant Genetic Resource (PGR) collections, have lacked access to high quality IT needed to document and manage their collections electronically. The Germplasm Resource Information System (GRI...

RNGR: A national resource for reforestation, restoration, and nursery professionals

Treesearch

Diane L. Haase; Jeremiah R. Pinto; R. Kasten Dumroese; George Hernandez; Bob Karrfalt; Ron Overton

2011-01-01

The Forest Service developed the national Reforestation, Nurseries, and Genetics Resources (RNGR) program to provide expert support to State, industrial, and private forest and conservation nurseries throughout the country. The RNGR program includes technical assistance to nurseries, research projects (to address seedling and field issues), and Internet sites. RNGR...

Use of genotyping-by-sequencing to determine the genetic structure in the medicinal plant chamomile, and to identify flowering time and alpha-bisabolol associated SNP-loci by genome-wide association mapping.

PubMed

Otto, Lars-Gernot; Mondal, Prodyut; Brassac, Jonathan; Preiss, Susanne; Degenhardt, Jörg; He, Sang; Reif, Jochen Christoph; Sharbel, Timothy Francis

2017-08-10

Chamomile (Matricaria recutita L.) has a long history of use in herbal medicine with various applications, and the flower heads contain numerous secondary metabolites which are medicinally active. In the major crop plants, next generation sequencing (NGS) approaches are intensely applied to exploit genetic resources, to develop genomic resources and to enhance breeding. Here, genotyping-by-sequencing (GBS) has been used in the non-model medicinal plant chamomile to evaluate the genetic structure of the cultivated varieties/populations, and to perform genome wide association study (GWAS) focusing on genes with large effect on flowering time and the medicinally important alpha-bisabolol content. GBS analysis allowed the identification of 6495 high-quality SNP-markers in our panel of 91 M. recutita plants from 33 origins (2-4 genotypes each) and 4 M. discoidea plants as outgroup, grown in the greenhouse in Gatersleben, Germany. M. recutita proved to be clearly distinct from the outgroup, as was demonstrated by different cluster and principal coordinate analyses using the SNP-markers. Chamomile genotypes from the same origin were mostly genetically similar. Model-based cluster analysis revealed one large group of tetraploid genotypes with low genetic differentiation including 39 plants from 14 origins. Tetraploids tended to display lower genetic diversity than diploids, probably reflecting their origin by artificial polyploidisation from only a limited set of genetic backgrounds. Analyses of flowering time demonstrated that diploids generally flowered earlier than tetraploids, and the analysis of alpha-bisabolol identified several tetraploid genotypes with a high content. GWAS identified highly significant (P < 0.01) SNPs for flowering time (9) and alpha-bisabolol (71). One sequence harbouring SNPs associated with flowering time was described to play a role in self-pollination in Arabidopsis thaliana, whereas four sequences harbouring SNPs associated with alpha-bisabolol were identified to be involved in plant biotic and abiotic stress response in various plants species. The first genomic resource for future applications to enhance breeding in chamomile was created, andanalyses of diversity will facilitate the exploitation of these genetic resources. The GWAS data pave the way for future research towards the genetics underlying important traits in chamomile, the identification of marker-trait associations, and development of reliable markers for practical breeding.

Regulation of Genetic Tests

MedlinePlus

... Informed Consent for Genomics Research Intellectual Property Online Bioethics Resources Privacy in Genomics Regulation of Genetic Tests ... Research Intellectual Property Issues in Genetics Archive Online Bioethics Resources Privacy in Genomics Regulation of Genetic Tests ...

Structural equation models based on multivariate diversity assessment of diploid and tetraploid hulled wheat species

USDA-ARS?s Scientific Manuscript database

Hulled wheats are largely untapped genetic resources with >10,000 years of genetic memory and diversity that can be used for wheat quality improvement, development of healthy products, and adaptation to climate change. Multivariate diversity was assessed in the diploid Triticum monococcum L. var mon...

Purification of high molecular weight genomic DNA from powdery mildew for long-read sequencing

USDA-ARS?s Scientific Manuscript database

The powdery mildew fungi are a group of economically important fungal plant pathogens. Relatively little is known about the molecular biology and genetics of these pathogens, in part due to a lack of well-developed genetic and genomic resources. These organisms have large, repetitive genomes, which ...

'HoneySweet' plum - a valuable genetically engineered fruit-tree cultivar and germplasm resource

USDA-ARS?s Scientific Manuscript database

‘HoneySweet’ is a plum variety developed through genetic engineering to be highly resistant to plum pox potyvirus (PPV), the causal agent of sharka disease, that threatens stone-fruit industries world-wide and most specifically, in Europe. Field testing for over 15 years in Europe has demonstrated ...

Landscape genetics of Persian walnut (Juglans regia L.) across its Asian range

Treesearch

Paola Pollegioni; Keith E. Woeste; Francesca Chiocchini; Irene Olimpieri; Virginia Tortolano; Jo Clark; Gabriel E. Hemery; Sergio Mapelli; Maria Emilla Malvolti

2014-01-01

Persian walnut (Juglans regia L) is an economically important species cultivated worldwide for its wood and nuts. Despite the increasing interest in the development of conservation strategies for walnut germplasm, an accurate and full-scale overview of wild genetic resources of J. regia has not been conducted because natural...

Genetic education for primary care providers

PubMed Central

Carroll, June C.; Rideout, Andrea L.; Wilson, Brenda J.; Allanson, Judith MD; Blaine, Sean M.; Esplen, Mary Jane; Farrell, Sandra A.; Graham, Gail E.; MacKenzie, Jennifer; Meschino, Wendy; Miller, Fiona; Prakash, Preeti; Shuman, Cheryl; Summers, Anne; Taylor, Sherry

2009-01-01

ABSTRACT OBJECTIVE To increase primary care providers’ awareness and use of genetic services; increase their knowledge of genetic issues; increase their confidence in core genetic competencies; change their attitudes toward genetic testing for hereditary diseases; and increase their confidence as primary care genetic resources. DESIGN Participants completed a workshop and 3 questionnaires: a baseline questionnaire, a survey that provided immediate feedback on the workshop itself, and a follow-up questionnaire 6 months later. SETTING Ontario. PARTICIPANTS Primary care providers suggested by deans of nursing, midwifery, family medicine, and obstetric programs, as well as coordinators of nurse practitioner programs, in Ontario and by the Ontario College of Family Physicians. INTERVENTION A complex educational intervention was developed, including an interactive workshop and PowerPoint educational modules on genetic topics for participants’ use (available at www.mtsinai.on.ca/FamMedGen/). MAIN OUTCOME MEASURES Awareness and use of genetic services, knowledge of genetics, confidence in core clinical genetic skills, attitudes toward genetic testing, and teaching activities related to genetics. RESULTS The workshop was attended by 29 participants; of those, 21 completed the baseline questionnaire and the 6-month follow-up questionnaire. There was no significant change found in awareness or reported use of genetic services. There was significant improvement in self-assessed knowledge of (P = .001) and confidence in (P = .005) skills related to adult-onset genetic disorders. There were significant increases in confidence in many core genetic competencies, including assessing risk of hereditary disorders (P = .033), deciding who should be offered referral for genetic counseling (P = .003), discussing prenatal testing options (P = .034), discussing benefits, risks, and limitations of genetic testing (P = .033), and describing what to expect at a genetic counseling session (P = .022). There was a significant increase in the number of primary care providers agreeing that genetic testing was beneficial in the management of adult-onset diseases (P = .031) and in their confidence in being primary care genetic resources for adult-onset genetic disorders (P = .006). CONCLUSION Educational interventions that include interactive peer resource workshops and educational modules can increase knowledge of and confidence in the core competencies needed for the delivery of genetic services in primary care. PMID:20008584

Surprisingly little population genetic structure in a fungus-associated beetle despite its exploitation of multiple hosts

PubMed Central

Wood, Corlett W; Donald, Hannah M; Formica, Vincent A; Brodie, Edmund D

2013-01-01

In heterogeneous environments, landscape features directly affect the structure of genetic variation among populations by functioning as barriers to gene flow. Resource-associated population genetic structure, in which populations that use different resources (e.g., host plants) are genetically distinct, is a well-studied example of how environmental heterogeneity structures populations. However, the pattern that emerges in a given landscape should depend on its particular combination of resources. If resources constitute barriers to gene flow, population differentiation should be lowest in homogeneous landscapes, and highest where resources exist in equal proportions. In this study, we tested whether host community diversity affects population genetic structure in a beetle (Bolitotherus cornutus) that exploits three sympatric host fungi. We collected B. cornutus from plots containing the three host fungi in different proportions and quantified population genetic structure in each plot using a panel of microsatellite loci. We found no relationship between host community diversity and population differentiation in this species; however, we also found no evidence of resource-associated differentiation, suggesting that host fungi are not substantial barriers to gene flow. Moreover, we detected no genetic differentiation among B. cornutus populations separated by several kilometers, even though a previous study demonstrated moderate genetic structure on the scale of a few hundred meters. Although we found no effect of community diversity on population genetic structure in this study, the role of host communities in the structuring of genetic variation in heterogeneous landscapes should be further explored in a species that exhibits resource-associated population genetic structure. PMID:23789061

Mapping public policy on genetics.

PubMed

Weisfeld, N E

2002-06-01

The mapping of the human genome and related advances in genetics are stimulating the development of public policies on genetics. Certain notions that currently prevail in public policy development overall--including the importance of protecting privacy of information, an interest in cost-effectiveness, and the power of the anecdote--will help determine the future of public policy on genetics. Information areas affected include discrimination by insurers and employers, confidentiality, genetic databanks, genetic testing in law enforcement, and court-ordered genetic testing in civil cases. Service issues address clinical standards, insurance benefits, allocation of resources, and screening of populations at risk. Supply issues encompass funding of research and clinical positions. Likely government actions include, among others: (1) Requiring individual consent for the disclosure of personal information, except when such consent would impose inordinate costs; (2) licensing genetic databases; (3) allowing courts to use personal information in cases where a refusal to use such information would offend the public; (4) mandating health insurers to pay for cost-effective genetic services; (5) funding pharmaceutical research to develop tailored products to prevent or treat diseases; and (6) funding training programs.

Conserving and managing the trees of the future: genetic resources for Pacific Northwest forests.

Treesearch

Sally Duncan

2003-01-01

Genetic resource management has historically called for altering the genetic structure of plant populations through selection for traits of interest such as rapid growth. Although this is still a principal component of tree breeding programs in the Pacific Northwest, managing genetic resources now also brings a clear focus on retaining a broad diversity within and...

Primary care providers' lived experiences of genetics in practice.

PubMed

Harding, Brittany; Webber, Colleen; Ruhland, Lucia; Dalgarno, Nancy; Armour, Christine M; Birtwhistle, Richard; Brown, Glenn; Carroll, June C; Flavin, Michael; Phillips, Susan; MacKenzie, Jennifer J

2018-04-26

To effectively translate genetic advances into practice, engagement of primary care providers (PCPs) is essential. Using a qualitative, phenomenological methodology, we analyzed key informant interviews and focus groups designed to explore perspectives of urban and rural PCPs. PCPs endorsed a responsibility to integrate genetics into their practices and expected advances in genetic medicine to expand. However, PCPs reported limited knowledge and difficulties accessing resources, experts, and continuing education. Rural practitioners' additional concerns included cost, distance, and poor patient engagement. PCPs' perspectives are crucial to develop relevant educational and systems-based interventions to further expand genetic medicine in primary care.

Nursing and genetic biobanks.

PubMed

Sanner, Jennifer E; Yu, Erica; Udtha, Malini; Williams, Pamela Holtzclaw

2013-12-01

Biobanks function as vital components in genetic research, which often requires large disease-based or population-based biospecimens and clinical data to study complex or rare diseases. Genetic biobanks aim to provide resources for translational research focusing on rapidly moving scientific findings from the laboratory into health care practice. The nursing profession must evolve as genetic biobanking practices advance. Nursing involvement in genetic biobanking practices comes with a distinct set of educational, ethical, and practice competencies. In response to these growing competency standards, nursing science developed a conceptual framework and continues to study ethical considerations to guide genetic biobanking initiatives. Copyright © 2013 Elsevier Inc. All rights reserved.

Studies on Monitoring and Tracking Genetic Resources: An Executive Summary

PubMed Central

Garrity, George M.; Thompson, Lorraine M.; Ussery, David W.; Paskin, Norman; Baker, Dwight; Desmeth, Philippe; Schindel, D.E.; Ong, P.S.

2009-01-01

The principles underlying fair and equitable sharing of benefits derived from the utilization of genetic resources are set out in Article 15 of the UN Convention on Biological Diversity, which stipulate that access to genetic resources is subject to the prior informed consent of the country where such resources are located and to mutually agreed terms regarding the sharing of benefits that could be derived from such access. One issue of particular concern for provider countries is how to monitor and track genetic resources once they have left the provider country and enter into use in a variety of forms. This report was commissioned to provide a detailed review of advances in DNA sequencing technologies, as those methods apply to identification of genetic resources, and the use of globally unique persistent identifiers for persistently linking to data and other forms of digital documentation that is linked to individual genetic resources. While the report was written for an audience with a mixture of technical, legal, and policy backgrounds it is relevant to the genomics community as it is an example of downstream application of genomics information. PMID:21304641

First TILLING Platform in Cucurbita pepo: A New Mutant Resource for Gene Function and Crop Improvement

PubMed Central

Vicente-Dólera, Nelly; Troadec, Christelle; Moya, Manuel; del Río-Celestino, Mercedes; Pomares-Viciana, Teresa; Bendahmane, Abdelhafid; Picó, Belén; Román, Belén; Gómez, Pedro

2014-01-01

Although the availability of genetic and genomic resources for Cucurbita pepo has increased significantly, functional genomic resources are still limited for this crop. In this direction, we have developed a high throughput reverse genetic tool: the first TILLING (Targeting Induced Local Lesions IN Genomes) resource for this species. Additionally, we have used this resource to demonstrate that the previous EMS mutant population we developed has the highest mutation density compared with other cucurbits mutant populations. The overall mutation density in this first C. pepo TILLING platform was estimated to be 1/133 Kb by screening five additional genes. In total, 58 mutations confirmed by sequencing were identified in the five targeted genes, thirteen of which were predicted to have an impact on the function of the protein. The genotype/phenotype correlation was studied in a peroxidase gene, revealing that the phenotype of seedling homozygous for one of the isolated mutant alleles was albino. These results indicate that the TILLING approach in this species was successful at providing new mutations and can address the major challenge of linking sequence information to biological function and also the identification of novel variation for crop breeding. PMID:25386735

Unlocking the genetic diversity of Creole wheats.

PubMed

Vikram, Prashant; Franco, Jorge; Burgueño-Ferreira, Juan; Li, Huihui; Sehgal, Deepmala; Saint Pierre, Carolina; Ortiz, Cynthia; Sneller, Clay; Tattaris, Maria; Guzman, Carlos; Sansaloni, Carolina Paola; Ellis, Mark; Fuentes-Davila, Guillermo; Reynolds, Matthew; Sonders, Kai; Singh, Pawan; Payne, Thomas; Wenzl, Peter; Sharma, Achla; Bains, Navtej Singh; Singh, Gyanendra Pratap; Crossa, José; Singh, Sukhwinder

2016-03-15

Climate change and slow yield gains pose a major threat to global wheat production. Underutilized genetic resources including landraces and wild relatives are key elements for developing high-yielding and climate-resilient wheat varieties. Landraces introduced into Mexico from Europe, also known as Creole wheats, are adapted to a wide range of climatic regimes and represent a unique genetic resource. Eight thousand four hundred and sixteen wheat landraces representing all dimensions of Mexico were characterized through genotyping-by-sequencing technology. Results revealed sub-groups adapted to specific environments of Mexico. Broadly, accessions from north and south of Mexico showed considerable genetic differentiation. However, a large percentage of landrace accessions were genetically very close, although belonged to different regions most likely due to the recent (nearly five centuries before) introduction of wheat in Mexico. Some of the groups adapted to extreme environments and accumulated high number of rare alleles. Core reference sets were assembled simultaneously using multiple variables, capturing 89% of the rare alleles present in the complete set. Genetic information about Mexican wheat landraces and core reference set can be effectively utilized in next generation wheat varietal improvement.

Development of a high-throughput SNP resource to advance genomic, genetic and breeding research in carrot (Daucus carota L.)

USDA-ARS?s Scientific Manuscript database

The rapid advancement in high-throughput SNP genotyping technologies along with next generation sequencing (NGS) platforms has decreased the cost, improved the quality of large-scale genome surveys, and allowed specialty crops with limited genomic resources such as carrot (Daucus carota) to access t...

Building a model: developing genomic resources for common milkweed (Asclepias syriaca) with low coverage genome sequencing

Treesearch

Shannon C.K. Straub; Mark Fishbein; Tatyana Livshult; Zachary Foster; Matthew Parks; Kevin Weitemier; Richard C. Cronn; Aaron Liston

2011-01-01

Milkweeds (Asclepias L.) have been extensively investigated in diverse areas of evolutionary biology and ecology; however, there are few genetic resources available to facilitate and compliment these studies. This study explored how low coverage genome sequencing of the common milkweed (Asclepias syriaca L.) could be useful in...

GRIN-Global: An International Project to Develop a Global Plant Genebank and Information Management System

USDA-ARS?s Scientific Manuscript database

The mission of the GRIN-Global Project is to create a new, scalable version of the Germplasm Resource Information System (GRIN) to provide the world’s crop genebanks with a powerful, flexible, easy-to-use plant genetic resource (PGR) information management system. The system will help safeguard PGR ...

GRIN-Global: An International Project to Develop a Global Plant Genebank and Information Management System

USDA-ARS?s Scientific Manuscript database

The mission of the GRIN-Global Project is to create a new, scalable version of the Germplasm Resource Information System (GRIN) to provide the world's crop genebanks with a powerful, flexible, easy-to-use plant genetic resource (PGR) information management system. The system will help safeguard PGR ...

GRIN-Global: An International Project to Develop a Global Plant Genebank and Information Management System

USDA-ARS?s Scientific Manuscript database

The mission of the GRIN-Global Project is to create a new, scalable version of the Germplasm Resource Information System (GRIN) to provide the world’s crop genebanks with a powerful, flexible, easy-to-use plant genetic resource (PGR) information management system. The system will help safeguard PGR...

GRIN-Global: An International Project to Develop a Global Plant Genebank Information Management System

USDA-ARS?s Scientific Manuscript database

The mission of the GRIN-Global Project is to create a new, scalable version of the Germplasm Resource Information System (GRIN) to provide the world’s crop genebanks with a powerful, flexible, easy-to-use plant genetic resource (PGR) information management system. The system will help safeguard PGR ...

The Diversity Outbred Mouse Population

PubMed Central

Churchill, Gary A.; Gatti, Daniel M.; Munger, Steven C.; Svenson, Karen L.

2012-01-01

The Diversity Outbred (DO) population is a heterogeneous stock derived from the same eight founder strains as the Collaborative Cross (CC) inbred strains. Genetically heterogeneous DO mice display a broad range of phenotypes. Natural levels of heterozygosity provide genetic buffering and, as a result, DO mice are robust and breed well. Genetic mapping analysis in the DO presents new challenges and opportunities. Specialized algorithms are required to reconstruct haplotypes from high-density SNP array data. The eight founder haplotypes can be combined into 36 possible diplotypes, which must be accommodated in QTL mapping analysis. Population structure of the DO must be taken into account here. Estimated allele effects of 8 founder haplotypes provide information that is not available in two-parent crosses and can dramatically reduce the number of candidate loci. Allele effects can also distinguish chance co-location of QTL from pleiotropy – which provides a basis for establishing causality in expression QTL studies. We recommended sample sizes of 200 to 800 mice for QTL mapping studies, larger than for traditional crosses. The CC inbred strains provide a resource for independent validation of DO mapping results. Genetic heterogeneity of the DO can provide a powerful advantage in our ability to generalize conclusions to other genetically diverse populations. Genetic diversity can also help to avoid the pitfall of identifying an idiosyncratic reaction that occurs only in a limited genetic context. Informatics tools and data resources associated with the CC, the DO, and their founder strains are developing rapidly. We anticipate a flood of new results to follow as our community begins to adopt and utilize these new genetic resource populations. PMID:22892839

Genetic relatedness among developing seeds and intra fruit seed abortion in Dalbergia sissoo (Fabaceae).

PubMed

Mohana, G S; Shaanker, R U; Ganeshaiah, K N; Dayanandan, S

2001-07-01

Dalbergia sissoo, a wind-dispersed tropical tree, exhibits high intrafruit seed abortion. Of the four to five ovules in the flower, generally one and occasionally two or three develop to maturity. It has been proposed that the seed abortion is a consequence of intense sibling competition for maternal resources and that this competition occurs as an inverse function of the genetic relatedness among the developing seeds. Accordingly, developing seeds compete intensely when they are genetically less related but tend to develop together when genetically more related. We tested this hypothesis by comparing the genetic similarity among the pairs of seeds developing within a pod with that among (a) random pairs from the pool of all seeds, (b) random pairs from single-seeded pods, and (c) random pairs from two-seeded pods, using both randomly amplified polymorphic DNA (RAPD) and isozymes in five trees. We found that the pairs of seeds developing within a pod are genetically more similar than any random pairs of seeds in a tree. Thus the formation of two-seeded pods appear to be associated with increased genetic relatedness among the developing seeds. We discuss the results in the context of possible fitness advantages and then discuss the possible mechanisms that promote tolerance among related seeds.

A community resource for exploring and utilizing genetic diversity in the USDA Pea Single Plant Plus Collection

USDA-ARS?s Scientific Manuscript database

Globally, pea (Pisum sativum L.) is an important temperate legume crop for food, feed, and fodder, and many breeding programs exist to develop cultivars adapted to these end uses. In order to conserve genetic diversity useful to researchers, large pea collections have been constructed by numerous na...

Construction of a Genetic Linkage Map and Identification of QTLs for Resistance to TSWV in Cultivated Peanut (Arachis hypagea L.)

USDA-ARS?s Scientific Manuscript database

A genetic linkage map is critical for identifying the QTL (quantitative trait loci) underling targeted traits. Over the last few years, progress has been made in marker development from multiple sources enabling the expansion of quality resources needed for genotyping applications in cultivated x cu...

Evaluation of water resources system vulnerability based on co-operative co-evolutionary genetic algorithm and projection pursuit model under the DPSIR framework

NASA Astrophysics Data System (ADS)

Zhao, Y.; Su, X. H.; Wang, M. H.; Li, Z. Y.; Li, E. K.; Xu, X.

2017-08-01

Water resources vulnerability control management is essential because it is related to the benign evolution of socio-economic, environmental and water resources system. Research on water resources system vulnerability is helpful to realization of water resources sustainable utilization. In this study, the DPSIR framework of driving forces-pressure-state-impact-response was adopted to construct the evaluation index system of water resources system vulnerability. Then the co-evolutionary genetic algorithm and projection pursuit were used to establish evaluation model of water resources system vulnerability. Tengzhou City in Shandong Province was selected as a study area. The system vulnerability was analyzed in terms of driving forces, pressure, state, impact and response on the basis of the projection value calculated by the model. The results show that the five components all belong to vulnerability Grade II, the vulnerability degree of impact and state were higher than other components due to the fierce imbalance in supply-demand and the unsatisfied condition of water resources utilization. It is indicated that the influence of high speed socio-economic development and the overuse of the pesticides have already disturbed the benign development of water environment to some extents. While the indexes in response represented lower vulnerability degree than the other components. The results of the evaluation model are coincident with the status of water resources system in the study area, which indicates that the model is feasible and effective.

New generation pharmacogenomic tools: a SNP linkage disequilibrium Map, validated SNP assay resource, and high-throughput instrumentation system for large-scale genetic studies.

PubMed

De La Vega, Francisco M; Dailey, David; Ziegle, Janet; Williams, Julie; Madden, Dawn; Gilbert, Dennis A

2002-06-01

Since public and private efforts announced the first draft of the human genome last year, researchers have reported great numbers of single nucleotide polymorphisms (SNPs). We believe that the availability of well-mapped, quality SNP markers constitutes the gateway to a revolution in genetics and personalized medicine that will lead to better diagnosis and treatment of common complex disorders. A new generation of tools and public SNP resources for pharmacogenomic and genetic studies--specifically for candidate-gene, candidate-region, and whole-genome association studies--will form part of the new scientific landscape. This will only be possible through the greater accessibility of SNP resources and superior high-throughput instrumentation-assay systems that enable affordable, highly productive large-scale genetic studies. We are contributing to this effort by developing a high-quality linkage disequilibrium SNP marker map and an accompanying set of ready-to-use, validated SNP assays across every gene in the human genome. This effort incorporates both the public sequence and SNP data sources, and Celera Genomics' human genome assembly and enormous resource ofphysically mapped SNPs (approximately 4,000,000 unique records). This article discusses our approach and methodology for designing the map, choosing quality SNPs, designing and validating these assays, and obtaining population frequency ofthe polymorphisms. We also discuss an advanced, high-performance SNP assay chemisty--a new generation of the TaqMan probe-based, 5' nuclease assay-and high-throughput instrumentation-software system for large-scale genotyping. We provide the new SNP map and validation information, validated SNP assays and reagents, and instrumentation systems as a novel resource for genetic discoveries.

[Research progress on mutation by spaceflight in medicinal plants breeding].

PubMed

Yan, Shuo; Gao, Wenyuan; Lu, Fuping; Zhao, Runhuai

2010-02-01

Space breeding in medicinal plants is special characteristics in China. Compared with other plants, in spite of a relatively small number, Medicinal plants have more obvious characteristics and advantages. Research on medicinal plants has also been carried into all aspects, such as biological traits, physiology and biochemistry, genomics, as well as differences in chemical composition, and chemical composition analysis is also involved. However, compared with other plants, especially crops and vegetables, biological research is an obvious deficiency, that is mainly reflected in the insufficient genetics and breeding researches, the stability of genetic traits from generation to generation were not followed up and in-depth study in breeding areas was not carried out. If medicinal plants resources from space with the genetic stability good quality were selected, it would address the problem of lack of resources and ease the pressure on wild resources of medicinal plants. It would at the same time play an important role in promoting the development of medicinal botany space breeding and the implementation of modernization of traditional Chinese medicine.

76 FR 35396 - Notice of Intent To Reestablish the National Genetic Resources Advisory Council, and Request for...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-06-17

... DEPARTMENT OF AGRICULTURE Agricultural Research Service Notice of Intent To Reestablish the National Genetic Resources Advisory Council, and Request for Nominations AGENCY: Agricultural Research... intent to reestablish the National Genetic Resources Advisory Council. The notice was published in the...

Proceedings of the third ISHS international symposium of plant genetic resources volume 1

USDA-ARS?s Scientific Manuscript database

The Third International ISHS Symposium on plant genetic resources occurred as Symposium 12 of the International Horticulture Congress in Lisbon, in August 2010. This symposium lasted4 days and emphasized new tools in plant genetic resource management. Six speakers gave invited presentations, and 30 ...

Proceedings of the third ISHS international symposium on plant genetic resources volume 2

USDA-ARS?s Scientific Manuscript database

The Third International ISHS Symposium on plant genetic resources occurred as Symposium 12 of the International Horticulture Congress in Lisbon, in August 2010. This symposium lasted4 days and emphasized new tools in plant genetic resource management. Six speakers gave invited presentations, and 30 ...

Genetic Simulation Tools for Post-Genome Wide Association Studies of Complex Diseases

PubMed Central

Amos, Christopher I.; Bafna, Vineet; Hauser, Elizabeth R.; Hernandez, Ryan D.; Li, Chun; Liberles, David A.; McAllister, Kimberly; Moore, Jason H.; Paltoo, Dina N.; Papanicolaou, George J.; Peng, Bo; Ritchie, Marylyn D.; Rosenfeld, Gabriel; Witte, John S.

2014-01-01

Genetic simulation programs are used to model data under specified assumptions to facilitate the understanding and study of complex genetic systems. Standardized data sets generated using genetic simulation are essential for the development and application of novel analytical tools in genetic epidemiology studies. With continuing advances in high-throughput genomic technologies and generation and analysis of larger, more complex data sets, there is a need for updating current approaches in genetic simulation modeling. To provide a forum to address current and emerging challenges in this area, the National Cancer Institute (NCI) sponsored a workshop, entitled “Genetic Simulation Tools for Post-Genome Wide Association Studies of Complex Diseases” at the National Institutes of Health (NIH) in Bethesda, Maryland on March 11-12, 2014. The goals of the workshop were to: (i) identify opportunities, challenges and resource needs for the development and application of genetic simulation models; (ii) improve the integration of tools for modeling and analysis of simulated data; and (iii) foster collaborations to facilitate development and applications of genetic simulation. During the course of the meeting the group identified challenges and opportunities for the science of simulation, software and methods development, and collaboration. This paper summarizes key discussions at the meeting, and highlights important challenges and opportunities to advance the field of genetic simulation. PMID:25371374

The coffee genome hub: a resource for coffee genomes

PubMed Central

Dereeper, Alexis; Bocs, Stéphanie; Rouard, Mathieu; Guignon, Valentin; Ravel, Sébastien; Tranchant-Dubreuil, Christine; Poncet, Valérie; Garsmeur, Olivier; Lashermes, Philippe; Droc, Gaëtan

2015-01-01

The whole genome sequence of Coffea canephora, the perennial diploid species known as Robusta, has been recently released. In the context of the C. canephora genome sequencing project and to support post-genomics efforts, we developed the Coffee Genome Hub (http://coffee-genome.org/), an integrative genome information system that allows centralized access to genomics and genetics data and analysis tools to facilitate translational and applied research in coffee. We provide the complete genome sequence of C. canephora along with gene structure, gene product information, metabolism, gene families, transcriptomics, syntenic blocks, genetic markers and genetic maps. The hub relies on generic software (e.g. GMOD tools) for easy querying, visualizing and downloading research data. It includes a Genome Browser enhanced by a Community Annotation System, enabling the improvement of automatic gene annotation through an annotation editor. In addition, the hub aims at developing interoperability among other existing South Green tools managing coffee data (phylogenomics resources, SNPs) and/or supporting data analyses with the Galaxy workflow manager. PMID:25392413

The Plant Genetic Engineering Laboratory For Desert Adaptation

NASA Astrophysics Data System (ADS)

Kemp, John D.; Phillips, Gregory C.

1985-11-01

The Plant Genetic Engineering Laboratory for Desert Adaptation (PGEL) is one of five Centers of Technical Excellence established as a part of the state of New Mexico's Rio Grande Research Corridor (RGRC). The scientific mission of PGEL is to bring innovative advances in plant biotechnology to bear on agricultural productivity in arid and semi-arid regions. Research activities focus on molecular and cellular genetics technology development in model systems, but also include stress physiology investigations and development of desert plant resources. PGEL interacts with the Los Alamos National Laboratory (LANL), a national laboratory participating in the RGRC. PGEL also has an economic development mission, which is being pursued through technology transfer activities to private companies and public agencies.

Cotton genetic resources and crop vulnerability

USDA-ARS?s Scientific Manuscript database

A report on the genetic vulnerability of cotton was provided to the National Genetic Resources Advisory Council. The report discussed crop vulnerabilities associated with emerging diseases, emerging pests, and a narrowing genetic base. To address these crop vulnerabilities, the report discussed the ...

Biological Diversity in the Patent System

PubMed Central

Oldham, Paul; Hall, Stephen; Forero, Oscar

2013-01-01

Biological diversity in the patent system is an enduring focus of controversy but empirical analysis of the presence of biodiversity in the patent system has been limited. To address this problem we text mined 11 million patent documents for 6 million Latin species names from the Global Names Index (GNI) established by the Global Biodiversity Information Facility (GBIF) and Encyclopedia of Life (EOL). We identified 76,274 full Latin species names from 23,882 genera in 767,955 patent documents. 25,595 species appeared in the claims section of 136,880 patent documents. This reveals that human innovative activity involving biodiversity in the patent system focuses on approximately 4% of taxonomically described species and between 0.8–1% of predicted global species. In this article we identify the major features of the patent landscape for biological diversity by focusing on key areas including pharmaceuticals, neglected diseases, traditional medicines, genetic engineering, foods, biocides, marine genetic resources and Antarctica. We conclude that the narrow focus of human innovative activity and ownership of genetic resources is unlikely to be in the long term interest of humanity. We argue that a broader spectrum of biodiversity needs to be opened up to research and development based on the principles of equitable benefit-sharing, respect for the objectives of the Convention on Biological Diversity, human rights and ethics. Finally, we argue that alternative models of innovation, such as open source and commons models, are required to open up biodiversity for research that addresses actual and neglected areas of human need. The research aims to inform the implementation of the 2010 Nagoya Protocol on Access to Genetic Resources and the Equitable Sharing of Benefits Arising from their Utilization and international debates directed to the governance of genetic resources. Our research also aims to inform debates under the Intergovernmental Committee on Intellectual Property and Genetic Resources, Traditional Knowledge and Folklore at the World Intellectual Property Organization. PMID:24265714

A new definition of Genetic Counseling: National Society of Genetic Counselors' Task Force report.

PubMed

Resta, Robert; Biesecker, Barbara Bowles; Bennett, Robin L; Blum, Sandra; Hahn, Susan Estabrooks; Strecker, Michelle N; Williams, Janet L

2006-04-01

The Genetic Counseling Definition Task Force of the National Society of Genetic Counselors (NSGC) developed the following definition of genetic counseling that was approved by the NSGC Board of Directors: Genetic counseling is the process of helping people understand and adapt to the medical, psychological and familial implications of genetic contributions to disease. This process integrates the following: Interpretation of family and medical histories to assess the chance of disease occurrence or recurrence. Education about inheritance, testing, management, prevention, resources and research. Counseling to promote informed choices and adaptation to the risk or condition. The definition was approved after a peer review process with input from the NSGC membership, genetic professional organizations, the NSGC legal counsel, and leaders of several national genetic advocacy groups.

Genetic data simulators and their applications: an overview

PubMed Central

Peng, Bo; Chen, Huann-Sheng; Mechanic, Leah E.; Racine, Ben; Clarke, John; Gillanders, Elizabeth; Feuer, Eric J.

2016-01-01

Computer simulations have played an indispensable role in the development and application of statistical models and methods for genetic studies across multiple disciplines. The need to simulate complex evolutionary scenarios and pseudo-datasets for various studies has fueled the development of dozens of computer programs with varying reliability, performance, and application areas. To help researchers compare and choose the most appropriate simulators for their studies, we have created the Genetic Simulation Resources (GSR) website, which allows authors of simulation software to register their applications and describe them with more than 160 defined attributes. This article summarizes the properties of 93 simulators currently registered at GSR and provides an overview of the development and applications of genetic simulators. Unlike other review articles that address technical issues or compare simulators for particular application areas, we focus on software development, maintenance, and features of simulators, often from a historical perspective. Publications that cite these simulators are used to summarize both the applications of genetic simulations and the utilization of simulators. PMID:25504286

Quantitative Genetics Identifies Cryptic Genetic Variation Involved in the Paternal Regulation of Seed Development

PubMed Central

Pires, Nuno D.; Bemer, Marian; Müller, Lena M.; Baroux, Célia; Spillane, Charles; Grossniklaus, Ueli

2016-01-01

Embryonic development requires a correct balancing of maternal and paternal genetic information. This balance is mediated by genomic imprinting, an epigenetic mechanism that leads to parent-of-origin-dependent gene expression. The parental conflict (or kinship) theory proposes that imprinting can evolve due to a conflict between maternal and paternal alleles over resource allocation during seed development. One assumption of this theory is that paternal alleles can regulate seed growth; however, paternal effects on seed size are often very low or non-existent. We demonstrate that there is a pool of cryptic genetic variation in the paternal control of Arabidopsis thaliana seed development. Such cryptic variation can be exposed in seeds that maternally inherit a medea mutation, suggesting that MEA acts as a maternal buffer of paternal effects. Genetic mapping using recombinant inbred lines, and a novel method for the mapping of parent-of-origin effects using whole-genome sequencing of segregant bulks, indicate that there are at least six loci with small, paternal effects on seed development. Together, our analyses reveal the existence of a pool of hidden genetic variation on the paternal control of seed development that is likely shaped by parental conflict. PMID:26811909

Quantitative Genetics Identifies Cryptic Genetic Variation Involved in the Paternal Regulation of Seed Development.

PubMed

Pires, Nuno D; Bemer, Marian; Müller, Lena M; Baroux, Célia; Spillane, Charles; Grossniklaus, Ueli

2016-01-01

Embryonic development requires a correct balancing of maternal and paternal genetic information. This balance is mediated by genomic imprinting, an epigenetic mechanism that leads to parent-of-origin-dependent gene expression. The parental conflict (or kinship) theory proposes that imprinting can evolve due to a conflict between maternal and paternal alleles over resource allocation during seed development. One assumption of this theory is that paternal alleles can regulate seed growth; however, paternal effects on seed size are often very low or non-existent. We demonstrate that there is a pool of cryptic genetic variation in the paternal control of Arabidopsis thaliana seed development. Such cryptic variation can be exposed in seeds that maternally inherit a medea mutation, suggesting that MEA acts as a maternal buffer of paternal effects. Genetic mapping using recombinant inbred lines, and a novel method for the mapping of parent-of-origin effects using whole-genome sequencing of segregant bulks, indicate that there are at least six loci with small, paternal effects on seed development. Together, our analyses reveal the existence of a pool of hidden genetic variation on the paternal control of seed development that is likely shaped by parental conflict.

Confidentiality, privacy, and security of genetic and genomic test information in electronic health records: points to consider.

PubMed

McGuire, Amy L; Fisher, Rebecca; Cusenza, Paul; Hudson, Kathy; Rothstein, Mark A; McGraw, Deven; Matteson, Stephen; Glaser, John; Henley, Douglas E

2008-07-01

As clinical genetics evolves, and we embark down the path toward more personalized and effective health care, the amount, detail, and complexity of genetic/genomic test information within the electronic health record will increase. This information should be appropriately protected to secure the trust of patients and to support interoperable electronic health information exchange. This article discusses characteristics of genetic/genomic test information, including predictive capability, immutability, and uniqueness, which should be considered when developing policies about information protection. Issues related to "genetic exceptionalism"; i.e., whether genetic/genomic test information should be treated differently from other medical information for purposes of data access and permissible use, are also considered. These discussions can help guide policy that will facilitate the biological and clinical resource development to support the introduction of this information into health care.

Putting the Pieces Together: Clinically Relevant Genetic and Genomic Resources for Hospitalists and Neonatologists.

PubMed

Miller, Rebecca; Khromykh, Alina; Babcock, Holly; Jenevein, Callie; Solomon, Benjamin D

2017-02-01

Genetic conditions are individually rare but are common in aggregate, and they often present in the neonatal and early pediatric periods. These conditions are often severe, can be difficult to diagnose and manage, and may heavily affect patients, families, health care systems, and society. Because of recent technological advances, the availability and uptake of genetic and genomic testing are increasing rapidly. However, there is a dearth of trained geneticists and genetic counselors to help guide and explain these conditions and relevant tests. To help hospitalists, neonatologists, and related practitioners navigate this complex and evolving field, we have compiled a list of free (mostly Web-based) resources relevant to the diagnosis and management of genetic conditions and related disorders. These resources, which we describe individually, can be useful for nongeneticist clinicians, and some also include material that can be used to explain concepts and conditions to patients or families. The resources presented are divided into the following categories (which overlap): general information, databases of genetic conditions, resources that can help generate differential diagnoses, databases of genetic testing laboratories (to help with logistics of ordering tests), information on newborn screening, and other resources. We also include a separate list of helpful textbooks and manuals. We conclude with 2 examples describing how some of these resources would be used by a pediatric hospitalist or neonatologist during the inpatient management of a child with a suspected genetic condition. Copyright © 2017 by the American Academy of Pediatrics.

Report on the 6th African Society of Human Genetics (AfSHG) Meeting, March 12-15, 2009, Yaounde, Cameroon.

PubMed

Sirugo, Giorgio; Williams, Scott M; Royal, Charmaine D M; Newport, Melanie J; Hennig, Branwen J; Mariani-Costantini, Renato; Buonaguro, Franco M; Velez Edwards, Digna R; Ibrahim, Muntaser; Soodyall, Himla; Wonkam, Ambroise; Ramesar, Raj; Rotimi, Charles N

2010-08-01

The African Society of Human Genetics (AfSHG), founded in 2003 with its inaugural meeting in Accra, Ghana,1 has the stated missions of (1) disseminating information about human genetics research in Africa, (2) establishing a mentorship network providing educational resources, including the development of appropriate technology transfer, (3) providing advocacy for human genetic research in Africa, and (4) encouraging collaborative research. Despite its young age, the AfSHG has developed a strong cadre of active researchers, both within and outside of Africa, with more than 400 members (from 16 countries across Africa as well as 8 other countries), and has held six successful meetings, five in Africa and one in the United States.

A High Fuel Consumption Efficiency Management Scheme for PHEVs Using an Adaptive Genetic Algorithm

PubMed Central

Lee, Wah Ching; Tsang, Kim Fung; Chi, Hao Ran; Hung, Faan Hei; Wu, Chung Kit; Chui, Kwok Tai; Lau, Wing Hong; Leung, Yat Wah

2015-01-01

A high fuel efficiency management scheme for plug-in hybrid electric vehicles (PHEVs) has been developed. In order to achieve fuel consumption reduction, an adaptive genetic algorithm scheme has been designed to adaptively manage the energy resource usage. The objective function of the genetic algorithm is implemented by designing a fuzzy logic controller which closely monitors and resembles the driving conditions and environment of PHEVs, thus trading off between petrol versus electricity for optimal driving efficiency. Comparison between calculated results and publicized data shows that the achieved efficiency of the fuzzified genetic algorithm is better by 10% than existing schemes. The developed scheme, if fully adopted, would help reduce over 600 tons of CO2 emissions worldwide every day. PMID:25587974

Implications of metal accumulation mechanisms to phytoremediation.

PubMed

Memon, Abdul R; Schröder, Peter

2009-03-01

Trace elements (heavy metals and metalloids) are important environmental pollutants, and many of them are toxic even at very low concentrations. Pollution of the biosphere with trace elements has accelerated dramatically since the Industrial Revolution. Primary sources are the burning of fossil fuels, mining and smelting of metalliferous ores, municipal wastes, agrochemicals, and sewage. In addition, natural mineral deposits containing particularly large quantities of heavy metals are found in many regions. These areas often support characteristic plant species thriving in metal-enriched environments. Whereas many species avoid the uptake of heavy metals from these soils, some of them can accumulate significantly high concentrations of toxic metals, to levels which by far exceed the soil levels. The natural phenomenon of heavy metal tolerance has enhanced the interest of plant ecologists, plant physiologists, and plant biologists to investigate the physiology and genetics of metal tolerance in specialized hyperaccumulator plants such as Arabidopsis halleri and Thlaspi caerulescens. In this review, we describe recent advances in understanding the genetic and molecular basis of metal tolerance in plants with special reference to transcriptomics of heavy metal accumulator plants and the identification of functional genes implied in tolerance and detoxification. Plants are susceptible to heavy metal toxicity and respond to avoid detrimental effects in a variety of different ways. The toxic dose depends on the type of ion, ion concentration, plant species, and stage of plant growth. Tolerance to metals is based on multiple mechanisms such as cell wall binding, active transport of ions into the vacuole, and formation of complexes with organic acids or peptides. One of the most important mechanisms for metal detoxification in plants appears to be chelation of metals by low-molecular-weight proteins such as metallothioneins and peptide ligands, the phytochelatins. For example, glutathione (GSH), a precursor of phytochelatin synthesis, plays a key role not only in metal detoxification but also in protecting plant cells from other environmental stresses including intrinsic oxidative stress reactions. In the last decade, tremendous developments in molecular biology and success of genomics have highly encouraged studies in molecular genetics, mainly transcriptomics, to identify functional genes implied in metal tolerance in plants, largely belonging to the metal homeostasis network. Analyzing the genetics of metal accumulation in these accumulator plants has been greatly enhanced through the wealth of tools and the resources developed for the study of the model plant Arabidopsis thaliana such as transcript profiling platforms, protein and metabolite profiling, tools depending on RNA interference (RNAi), and collections of insertion line mutants. To understand the genetics of metal accumulation and adaptation, the vast arsenal of resources developed in A. thaliana could be extended to one of its closest relatives that display the highest level of adaptation to high metal environments such as A. halleri and T. caerulescens. This review paper deals with the mechanisms of heavy metal accumulation and tolerance in plants. Detailed information has been provided for metal transporters, metal chelation, and oxidative stress in metal-tolerant plants. Advances in phytoremediation technologies and the importance of metal accumulator plants and strategies for exploring these immense and valuable genetic and biological resources for phytoremediation are discussed. A number of species within the Brassicaceae family have been identified as metal accumulators. To understand fully the genetics of metal accumulation, the vast genetic resources developed in A. thaliana must be extended to other metal accumulator species that display traits absent in this model species. A. thaliana microarray chips could be used to identify differentially expressed genes in metal accumulator plants in Brassicaceae. The integration of resources obtained from model and wild species of the Brassicaceae family will be of utmost importance, bringing most of the diverse fields of plant biology together such as functional genomics, population genetics, phylogenetics, and ecology. Further development of phytoremediation requires an integrated multidisciplinary research effort that combines plant biology, genetic engineering, soil chemistry, soil microbiology, as well as agricultural and environmental engineering.

Integration of georeferencing, habitat, sampling, and genetic data for documentation of wild plant genetic resources

USDA-ARS?s Scientific Manuscript database

Plant genetic resource collections provide novel materials to the breeding and research communities. Availability of detailed documentation of passport, phenotypic, and genetic data increases the value of the genebank accessions. Inclusion of georeferenced sources, habitats, and sampling data in co...

An Online Resource of Digital Stories About Cancer Genetics: Qualitative Study of Patient Preferences and Information Needs

PubMed Central

Mundy, Lisa; Hilgart, Jennifer

2011-01-01

Background The Cancer Genetics Service for Wales (CGSW) was established in 1998 as an all-Wales service for individuals with concerns about their family history of cancer. CGSW offers a range of services such as risk assessment, genetic counseling, and genetic testing. Individuals referred to cancer genetics services often have unmet information and support needs, and they value access to practical and experiential information from other patients and health professionals. As a result of the lifelong nature of genetic conditions, a fundamental challenge is to meet the ongoing needs of these patients by providing easily accessible and reliable information. Objectives Our aims were to explore how the long-term information and support needs of CGSW patients could be met and to assess whether an online bank of digital stories about cancer genetics would be acceptable to patients. Methods In 2009, CGSW organized patient panels across Wales. During these events, 169 patients were asked for their feedback about a potential online resource of digital stories from CGSW patients and staff. A total of 75 patients registered to take part in the project and 23 people from across Wales agreed to share their story. All participants took part in a follow-up interview. Results Patient preferences for an online collection of cancer genetics stories were collected at the patient panels. Key topics to be covered by the stories were identified, and this feedback informed the development of the website to ensure that patients’ needs would be met. The 23 patient storytellers were aged between 28 and 75 years, and 19 were female. The digital stories reflect patients’ experiences within CGSW and the implications of living with or at risk of cancer. Follow-up interviews with patient storytellers showed that they shared their experiences as a means of helping other patients and to increase understanding of the cancer genetics service. Digital stories were also collected from 12 members of staff working at CGSW. The digital stories provide reliable and easily accessible information about cancer genetics and are hosted on the StoryBank website (www.cancergeneticsstorybank.co.uk). Conclusions The Internet is one mechanism through which the long-term information and support needs of cancer genetics patients can be met. The StoryBank is one of the first places where patient and staff stories have been allied to every aspect of a patient pathway through a service and provides patients with an experiential perspective of the cancer genetics “journey.” The StoryBank was developed in direct response to patient feedback and is an innovative example of patient involvement in service development. The stories are a useful resource for newly referred patients, current patients, the general public, and health care professionals. PMID:22057223

Black raspberry genetic and genomic resources development

USDA-ARS?s Scientific Manuscript database

This study incorporates field and laboratory components to advance and streamline identification of a variety of traits of economic interest and to develop molecular markers for marker assisted breeding of black raspberry (Rubus occidentalis). A lack of adapted, disease resistant cultivars has led t...

Developing black raspberry genetic and genomic resources

USDA-ARS?s Scientific Manuscript database

This study incorporates field and laboratory components to advance and streamline identification of a variety of traits of economic interest and to develop molecular markers for marker assisted breeding of black raspberry (Rubus occidentalis). A lack of adapted, disease resistant cultivars has led t...

American Epilepsy Society

MedlinePlus

... Epilepsy Society CLINICAL RESOURCES FAQs GUIDELINES IOM EPILEPSY MEDICAL MARIJUANA SUDEP SURGERY DEVICES GENETICS TREATMENTS Drug Alerts and ... RESOURCES Navigation CLINICAL RESOURCES FAQs GUIDELINES IOM EPILEPSY MEDICAL MARIJUANA SUDEP SURGERY DEVICES GENETICS TREATMENTS Drug Alerts and ...

Genomic analyses of the CAM plant pineapple.

PubMed

Zhang, Jisen; Liu, Juan; Ming, Ray

2014-07-01

The innovation of crassulacean acid metabolism (CAM) photosynthesis in arid and/or low CO2 conditions is a remarkable case of adaptation in flowering plants. As the most important crop that utilizes CAM photosynthesis, the genetic and genomic resources of pineapple have been developed over many years. Genetic diversity studies using various types of DNA markers led to the reclassification of the two genera Ananas and Pseudananas and nine species into one genus Ananas and two species, A. comosus and A. macrodontes with five botanical varieties in A. comosus. Five genetic maps have been constructed using F1 or F2 populations, and high-density genetic maps generated by genotype sequencing are essential resources for sequencing and assembling the pineapple genome and for marker-assisted selection. There are abundant expression sequence tag resources but limited genomic sequences in pineapple. Genes involved in the CAM pathway has been analysed in several CAM plants but only a few of them are from pineapple. A reference genome of pineapple is being generated and will accelerate genetic and genomic research in this major CAM crop. This reference genome of pineapple provides the foundation for studying the origin and regulatory mechanism of CAM photosynthesis, and the opportunity to evaluate the classification of Ananas species and botanical cultivars. © The Author 2014. Published by Oxford University Press on behalf of the Society for Experimental Biology. All rights reserved. For permissions, please email: journals.permissions@oup.com.

A Road Map for 21st Century Genetic Restoration: Gene Pool Enrichment of the Black-Footed Ferret.

PubMed

Wisely, Samantha M; Ryder, Oliver A; Santymire, Rachel M; Engelhardt, John F; Novak, Ben J

2015-01-01

Interspecies somatic cell nuclear transfer (iSCNT) could benefit recovery programs of critically endangered species but must be weighed with the risks of failure. To weigh the risks and benefits, a decision-making process that evaluates progress is needed. Experiments that evaluate the efficiency and efficacy of blastocyst, fetal, and post-parturition development are necessary to determine the success or failure or species-specific iSCNT programs. Here, we use the black-footed ferret (Mustela nigripes) as a case study for evaluating this emerging biomedical technology as a tool for genetic restoration. The black-footed ferret has depleted genetic variation yet genome resource banks contain genetic material of individuals not currently represented in the extant lineage. Thus, genetic restoration of the species is in theory possible and could help reduce the persistent erosion of genetic diversity from drift. Extensive genetic, genomic, and reproductive science tools have previously been developed in black-footed ferrets and would aid in the process of developing an iSCNT protocol for this species. Nonetheless, developing reproductive cloning will require years of experiments and a coordinated effort among recovery partners. The information gained from a well-planned research effort with the goal of genetic restoration via reproductive cloning could establish a 21st century model for evaluating and implementing conservation breeding that would be applicable to other genetically impoverished species. © The American Genetic Association. 2015.

Genetics Home Reference: Saethre-Chotzen syndrome

MedlinePlus

... Saethre-Chotzen syndrome Johns Hopkins Collaboration for Craniofacial Development and Disorders MalaCards: saethre-chotzen syndrome Orphanet: Saethre-Chotzen syndrome Seattle Children's Hospital and Regional Medical Center Patient Support and Advocacy Resources (4 ...

Best practices for fungal germplasm repositories and perspectives on their implementation.

PubMed

Wiest, Aric; Schnittker, Robert; Plamann, Mike; McCluskey, Kevin

2012-02-01

In over 50 years, the Fungal Genetics Stock Center has grown to become a world-recognized biological resource center. Along with this growth comes the development and implementation of myriad practices for the management and curation of a diverse collection of filamentous fungi, yeast, and molecular genetic tools for working with the fungi. These practices include techniques for the testing, manipulation, and preservation of individual fungal isolates as well as for processing of thousands of isolates in parallel. In addition to providing accurate record keeping, an electronic managements system allows the observation of trends in strain distribution and in sample characteristics. Because many ex situ fungal germplasm repositories around the world share similar objectives, best-practice guidelines have been developed by a number of organizations such as the Organization for Economic Cooperation and Development or the International Society for Biological and Environmental Repositories. These best-practice guidelines provide a framework for the successful operation of collections and promote the development and interactions of biological resource centers around the world.

Molecular Study of the Amazonian Macabea Cattle History.

PubMed

Vargas, Julio; Landi, Vincenzo; Martínez, Amparo; Gómez, Mayra; Camacho, María Esperanza; Álvarez, Luz Ángela; Aguirre, Lenin; Delgado, Juan Vicente

2016-01-01

Macabea cattle are the only Bos taurus breed that have adapted to the wet tropical conditions of the Amazon. This breed has integrated into the culture of the indigenous Shuar-Asuar nations probably since its origins, being one of the few European zoogenetic resources assimilated by the deep-jungle Amazon communities. Despite its potential for local endogenous sustainable development, this breed is currently endangered. The present study used molecular genetics tools to investigate the within- and between-breeds diversity, in order to characterize the breed population, define its associations with other breeds, and infer its origin and evolution. The within-breed genetic diversity showed high values, as indicated by all genetic parameters, such as the mean number of alleles (MNA = 7.25±2.03), the observed heterozygosity (Ho = 0.72±0.02) and the expected heterozygosity (He = 0.72±0.02). The between-breeds diversity analysis, which included factorial correspondence analysis, Reynolds genetic distance, neighbor-joining analysis, and genetic structure analysis, showed that the Macabea breed belongs to the group of the American Creoles, with a Southern-Spain origin. Our outcomes demonstrated that the Macabea breed has a high level of purity and null influences of exotic cosmopolitan breeds with European or Asiatic origin. This breed is an important zoogenetic resource of Ecuador, with relevant and unique attributes; therefore, there is an urgent need to develop conservation strategies for the Macabea breed.

Molecular Study of the Amazonian Macabea Cattle History

PubMed Central

Vargas, Julio; Martínez, Amparo; Gómez, Mayra; Camacho, María Esperanza; Álvarez, Luz Ángela; Aguirre, Lenin; Delgado, Juan Vicente

2016-01-01

Macabea cattle are the only Bos taurus breed that have adapted to the wet tropical conditions of the Amazon. This breed has integrated into the culture of the indigenous Shuar-Asuar nations probably since its origins, being one of the few European zoogenetic resources assimilated by the deep-jungle Amazon communities. Despite its potential for local endogenous sustainable development, this breed is currently endangered. The present study used molecular genetics tools to investigate the within- and between-breeds diversity, in order to characterize the breed population, define its associations with other breeds, and infer its origin and evolution. The within-breed genetic diversity showed high values, as indicated by all genetic parameters, such as the mean number of alleles (MNA = 7.25±2.03), the observed heterozygosity (Ho = 0.72±0.02) and the expected heterozygosity (He = 0.72±0.02). The between-breeds diversity analysis, which included factorial correspondence analysis, Reynolds genetic distance, neighbor-joining analysis, and genetic structure analysis, showed that the Macabea breed belongs to the group of the American Creoles, with a Southern-Spain origin. Our outcomes demonstrated that the Macabea breed has a high level of purity and null influences of exotic cosmopolitan breeds with European or Asiatic origin. This breed is an important zoogenetic resource of Ecuador, with relevant and unique attributes; therefore, there is an urgent need to develop conservation strategies for the Macabea breed. PMID:27776178

Resources for Genetic and Genomic Analysis of Emerging Pathogen Acinetobacter baumannii

PubMed Central

Ramage, Elizabeth; Weiss, Eli J.; Radey, Matthew; Hayden, Hillary S.; Held, Kiara G.; Huse, Holly K.; Zurawski, Daniel V.; Brittnacher, Mitchell J.; Manoil, Colin

2015-01-01

ABSTRACT Acinetobacter baumannii is a Gram-negative bacterial pathogen notorious for causing serious nosocomial infections that resist antibiotic therapy. Research to identify factors responsible for the pathogen's success has been limited by the resources available for genome-scale experimental studies. This report describes the development of several such resources for A. baumannii strain AB5075, a recently characterized wound isolate that is multidrug resistant and displays robust virulence in animal models. We report the completion and annotation of the genome sequence, the construction of a comprehensive ordered transposon mutant library, the extension of high-coverage transposon mutant pool sequencing (Tn-seq) to the strain, and the identification of the genes essential for growth on nutrient-rich agar. These resources should facilitate large-scale genetic analysis of virulence, resistance, and other clinically relevant traits that make A. baumannii a formidable public health threat. IMPORTANCE Acinetobacter baumannii is one of six bacterial pathogens primarily responsible for antibiotic-resistant infections that have become the scourge of health care facilities worldwide. Eliminating such infections requires a deeper understanding of the factors that enable the pathogen to persist in hospital environments, establish infections, and resist antibiotics. We present a set of resources that should accelerate genome-scale genetic characterization of these traits for a reference isolate of A. baumannii that is highly virulent and representative of current outbreak strains. PMID:25845845

Genetics Home Reference: McCune-Albright syndrome

MedlinePlus

... while other cells have the mutated version. This phenomenon is called mosaicism . The severity of this disorder ... 1 link) Eunice Kennedy Shriver National Institute for Child Health and Human Development Educational Resources (3 links) ...

Genetics Home Reference: Myhre syndrome

MedlinePlus

... features of autism spectrum disorder affecting communication and social interaction. Hearing loss occurs in most people with Myhre ... Kennedy Shriver National Institute of Child Health and Human Development: Intellectual and Developmental Disabilities Educational Resources (6 ...

Biobanking genetic material for agricultural animal species

USDA-ARS?s Scientific Manuscript database

Biobanking animal germplasm and tissues is a major component of conserving genetic resources. Effectively constructing such gene banks requires an understanding and evaluation of genetic resources, the ability to conserve various tissues through cryopreservation, and a robust information technology ...

Agricultural biotechnologies in developing countries and their possible contribution to food security.

PubMed

Ruane, John; Sonnino, Andrea

2011-12-20

Latest FAO figures indicate that an estimated 925 million people are undernourished in 2010, representing almost 16% of the population in developing countries. Looking to the future, there are also major challenges ahead from the rapidly changing socio-economic environment (increasing world population and urbanisation, and dietary changes) and climate change. Promoting agriculture in developing countries is the key to achieving food security, and it is essential to act in four ways: to increase investment in agriculture, broaden access to food, improve governance of global trade, and increase productivity while conserving natural resources. To enable the fourth action, the suite of technological options for farmers should be as broad as possible, including agricultural biotechnologies. Agricultural biotechnologies represent a broad range of technologies used in food and agriculture for the genetic improvement of plant varieties and animal populations, characterisation and conservation of genetic resources, diagnosis of plant or animal diseases and other purposes. Discussions about agricultural biotechnology have been dominated by the continuing controversy surrounding genetic modification and its resulting products, genetically modified organisms (GMOs). The polarised debate has led to non-GMO biotechnologies being overshadowed, often hindering their development and application. Extensive documentation from the FAO international technical conference on Agricultural Biotechnologies in Developing Countries (ABDC-10), that took place in Guadalajara, Mexico, on 1-4 March 2010, gave a very good overview of the many ways that different agricultural biotechnologies are being used to increase productivity and conserve natural resources in the crop, livestock, fishery, forestry and agro-industry sectors in developing countries. The conference brought together about 300 policy-makers, scientists and representatives of intergovernmental and international non-governmental organisations, including delegations from 42 FAO Member States. At the end of ABDC-10, the Member States reached a number of key conclusions, agreeing, inter alia, that FAO and other relevant international organisations and donors should significantly increase their efforts to support the strengthening of national capacities in the development and appropriate use of pro-poor agricultural biotechnologies. Copyright © 2011 FAO. Published by Elsevier B.V. All rights reserved.

The conservation of forest genetic resources: case histories from Canada, Mexico, and the United States

Treesearch

F. Thomas Ledig; J. Jesús Vargas-Hernández; Kurt H. Johnsen

1998-01-01

The genetic codes of living organisms are natural resources no less than soil, air, and water. Genetic resources-from nucleotide sequences in DNA to selected genotypes, populations, and species-are the raw material in forestry: for breeders, for the forest manager who produces an economic crop, for society that reaps the environmental benefits provided by forests, and...

The Relationship between Conservation Policy and Aquatic Genetic Resources. In: T.R. Tiersch and C.C. Green (eds.) Cryopreservation in Aquatic Species, 2nd Edition. World Aquaculture Society, Baton Rouge, LA.

USDA-ARS?s Scientific Manuscript database

Globally there is an increased awareness of how important genetic resources are for all forms of agriculture. This awareness has resulted in questions concerning the policies countries and the international community should pursue to ensure the sustainable use of diverse genetic resources. For aquac...

The Collaborative Cross at Oak Ridge National Laboratory: developing a powerful resource for systems genetics

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chesler, Elissa J; Branstetter, Lisa R; Churchill, Gary A

2008-01-01

Complex traits and disease co-morbidity in humans and in model organisms are the result of naturally occurring polymorphisms that interact with each other and with the environment. To ensure the availability of the resources needed to investigate biomolecular networks and ultimately systems level phenotypes, we have initiated breeding of a new genetic reference population of mice, the Collaborative Cross. This population has been designed to optimally support systems genetics analysis. Its novel and important features include high levels of genetic diversity, a large population size to ensure sufficient power in high-dimensional studies, and high mapping precision through accumulation of independentmore » recombination events. Implementation of the Collaborative Cross has been in progress at the Oak Ridge National Laboratory (ORNL) since May 2005. This is achieved through a software assisted breeding program with fully traceable lineages, performed in a uniform environment. Currently, there are 650 lines in production with almost 200 lines over seven generations of inbreeding. Retired breeders enter a high-throughput phenotyping protocol and DNA samples are banked for analysis of recombination history, allele loss, and population structure. Herein we present a progress report of the Collaborative Cross breeding program at ORNL and a description of the kinds of investigations that this resource will support.« less

A Road Map for 21st Century Genetic Restoration: Gene Pool Enrichment of the Black-Footed Ferret

PubMed Central

Ryder, Oliver A.; Santymire, Rachel M.; Engelhardt, John F.; Novak, Ben J.

2015-01-01

Interspecies somatic cell nuclear transfer (iSCNT) could benefit recovery programs of critically endangered species but must be weighed with the risks of failure. To weigh the risks and benefits, a decision-making process that evaluates progress is needed. Experiments that evaluate the efficiency and efficacy of blastocyst, fetal, and post-parturition development are necessary to determine the success or failure or species-specific iSCNT programs. Here, we use the black-footed ferret (Mustela nigripes) as a case study for evaluating this emerging biomedical technology as a tool for genetic restoration. The black-footed ferret has depleted genetic variation yet genome resource banks contain genetic material of individuals not currently represented in the extant lineage. Thus, genetic restoration of the species is in theory possible and could help reduce the persistent erosion of genetic diversity from drift. Extensive genetic, genomic, and reproductive science tools have previously been developed in black-footed ferrets and would aid in the process of developing an iSCNT protocol for this species. Nonetheless, developing reproductive cloning will require years of experiments and a coordinated effort among recovery partners. The information gained from a well-planned research effort with the goal of genetic restoration via reproductive cloning could establish a 21st century model for evaluating and implementing conservation breeding that would be applicable to other genetically impoverished species. PMID:26304983

EHR based Genetic Testing Knowledge Base (iGTKB) Development

PubMed Central

2015-01-01

Background The gap between a large growing number of genetic tests and a suboptimal clinical workflow of incorporating these tests into regular clinical practice poses barriers to effective reliance on advanced genetic technologies to improve quality of healthcare. A promising solution to fill this gap is to develop an intelligent genetic test recommendation system that not only can provide a comprehensive view of genetic tests as education resources, but also can recommend the most appropriate genetic tests to patients based on clinical evidence. In this study, we developed an EHR based Genetic Testing Knowledge Base for Individualized Medicine (iGTKB). Methods We extracted genetic testing information and patient medical records from EHR systems at Mayo Clinic. Clinical features have been semi-automatically annotated from the clinical notes by applying a Natural Language Processing (NLP) tool, MedTagger suite. To prioritize clinical features for each genetic test, we compared odds ratio across four population groups. Genetic tests, genetic disorders and clinical features with their odds ratios have been applied to establish iGTKB, which is to be integrated into the Genetic Testing Ontology (GTO). Results Overall, there are five genetic tests operated with sample size greater than 100 in 2013 at Mayo Clinic. A total of 1,450 patients who was tested by one of the five genetic tests have been selected. We assembled 243 clinical features from the Human Phenotype Ontology (HPO) for these five genetic tests. There are 60 clinical features with at least one mention in clinical notes of patients taking the test. Twenty-eight clinical features with high odds ratio (greater than 1) have been selected as dominant features and deposited into iGTKB with their associated information about genetic tests and genetic disorders. Conclusions In this study, we developed an EHR based genetic testing knowledge base, iGTKB. iGTKB will be integrated into the GTO by providing relevant clinical evidence, and ultimately to support development of genetic testing recommendation system, iGenetics. PMID:26606281

EHR based Genetic Testing Knowledge Base (iGTKB) Development.

PubMed

Zhu, Qian; Liu, Hongfang; Chute, Christopher G; Ferber, Matthew

2015-01-01

The gap between a large growing number of genetic tests and a suboptimal clinical workflow of incorporating these tests into regular clinical practice poses barriers to effective reliance on advanced genetic technologies to improve quality of healthcare. A promising solution to fill this gap is to develop an intelligent genetic test recommendation system that not only can provide a comprehensive view of genetic tests as education resources, but also can recommend the most appropriate genetic tests to patients based on clinical evidence. In this study, we developed an EHR based Genetic Testing Knowledge Base for Individualized Medicine (iGTKB). We extracted genetic testing information and patient medical records from EHR systems at Mayo Clinic. Clinical features have been semi-automatically annotated from the clinical notes by applying a Natural Language Processing (NLP) tool, MedTagger suite. To prioritize clinical features for each genetic test, we compared odds ratio across four population groups. Genetic tests, genetic disorders and clinical features with their odds ratios have been applied to establish iGTKB, which is to be integrated into the Genetic Testing Ontology (GTO). Overall, there are five genetic tests operated with sample size greater than 100 in 2013 at Mayo Clinic. A total of 1,450 patients who was tested by one of the five genetic tests have been selected. We assembled 243 clinical features from the Human Phenotype Ontology (HPO) for these five genetic tests. There are 60 clinical features with at least one mention in clinical notes of patients taking the test. Twenty-eight clinical features with high odds ratio (greater than 1) have been selected as dominant features and deposited into iGTKB with their associated information about genetic tests and genetic disorders. In this study, we developed an EHR based genetic testing knowledge base, iGTKB. iGTKB will be integrated into the GTO by providing relevant clinical evidence, and ultimately to support development of genetic testing recommendation system, iGenetics.

Black raspberry genomic and genetic resource development to enable cultivar improvement

USDA-ARS?s Scientific Manuscript database

This project incorporates use of phenotypic, genotypic and genomic data to advance and streamline identification of traits of economic interest and to develop molecular markers for marker assisted breeding of black raspberry (Rubus occidentalis L.). A lack of adapted, disease resistant cultivars has...

Possibilities and pitfalls for modern biotechnology in the development of African genetic toxicology.

PubMed

Anwar, Wagida A

2005-09-01

Developing countries are currently going through a transitional phase facing the new challenges of globalization and its potential negative impact. Research policy should highlight the need to mobilize resources for human resource development, networking, improved research culture, information sharing, and pragmatic use of research findings. Advancement in molecular genetics whether at the educational or research level should greatly progress in developing countries so as to improve diagnosis, treatment, understanding of disease risk factors, and prevention. Currently, there is a growing interest to genetic toxicology research, the use of different biomarkers, and genetic susceptibility testing, which can contribute effectively in risk assessment. Africa has unique environmental exposures and public health circumstances, which make it ideal for environmental mutagenicity and carcinogenicity research. There are exposures to chemical genotoxicants (e.g., automobile exhaust, pesticides, metals, and cytotoxic drugs) and to lifestyle factors (e.g., consumption of tobacco products) that have been linked to the expression of biological effects and to increased risk for cancer. Infections can be associated with cancer development when the environmental factors interact with the infection and lead to the enhancement of the carcinogenic process. The high prevalence of viral pathogens and the improper use of pesticides may endanger biological functions beyond those for which they originally manufactured. Biomarkers are used to detect the effects of pesticides before adverse clinical health occurs. The scientific community plays a crucial role in understanding the environmental causes of human health problems and through its collaboration with communities, industries, and government agencies can help in resolving health problems.

Possibilities and pitfalls for modern biotechnology in the development of African genetic toxicology

DOE Office of Scientific and Technical Information (OSTI.GOV)

Anwar, Wagida A.

2005-09-01

Developing countries are currently going through a transitional phase facing the new challenges of globalization and its potential negative impact. Research policy should highlight the need to mobilize resources for human resource development, networking, improved research culture, information sharing, and pragmatic use of research findings. Advancement in molecular genetics whether at the educational or research level should greatly progress in developing countries so as to improve diagnosis, treatment, understanding of disease risk factors, and prevention. Currently, there is a growing interest to genetic toxicology research, the use of different biomarkers, and genetic susceptibility testing, which can contribute effectively in riskmore » assessment. Africa has unique environmental exposures and public health circumstances, which make it ideal for environmental mutagenicity and carcinogenicity research. There are exposures to chemical genotoxicants (e.g., automobile exhaust, pesticides, metals, and cytotoxic drugs) and to lifestyle factors (e.g., consumption of tobacco products) that have been linked to the expression of biological effects and to increased risk for cancer. Infections can be associated with cancer development when the environmental factors interact with the infection and lead to the enhancement of the carcinogenic process. The high prevalence of viral pathogens and the improper use of pesticides may endanger biological functions beyond those for which they originally manufactured. Biomarkers are used to detect the effects of pesticides before adverse clinical health occurs. The scientific community plays a crucial role in understanding the environmental causes of human health problems and through its collaboration with communities, industries, and government agencies can help in resolving health problems.« less

Low cost and open source multi-fluorescence imaging system for teaching and research in biology and bioengineering.

PubMed

Nuñez, Isaac; Matute, Tamara; Herrera, Roberto; Keymer, Juan; Marzullo, Timothy; Rudge, Timothy; Federici, Fernán

2017-01-01

The advent of easy-to-use open source microcontrollers, off-the-shelf electronics and customizable manufacturing technologies has facilitated the development of inexpensive scientific devices and laboratory equipment. In this study, we describe an imaging system that integrates low-cost and open-source hardware, software and genetic resources. The multi-fluorescence imaging system consists of readily available 470 nm LEDs, a Raspberry Pi camera and a set of filters made with low cost acrylics. This device allows imaging in scales ranging from single colonies to entire plates. We developed a set of genetic components (e.g. promoters, coding sequences, terminators) and vectors following the standard framework of Golden Gate, which allowed the fabrication of genetic constructs in a combinatorial, low cost and robust manner. In order to provide simultaneous imaging of multiple wavelength signals, we screened a series of long stokes shift fluorescent proteins that could be combined with cyan/green fluorescent proteins. We found CyOFP1, mBeRFP and sfGFP to be the most compatible set for 3-channel fluorescent imaging. We developed open source Python code to operate the hardware to run time-lapse experiments with automated control of illumination and camera and a Python module to analyze data and extract meaningful biological information. To demonstrate the potential application of this integral system, we tested its performance on a diverse range of imaging assays often used in disciplines such as microbial ecology, microbiology and synthetic biology. We also assessed its potential use in a high school environment to teach biology, hardware design, optics, and programming. Together, these results demonstrate the successful integration of open source hardware, software, genetic resources and customizable manufacturing to obtain a powerful, low cost and robust system for education, scientific research and bioengineering. All the resources developed here are available under open source licenses.

Low cost and open source multi-fluorescence imaging system for teaching and research in biology and bioengineering

PubMed Central

Herrera, Roberto; Keymer, Juan; Marzullo, Timothy; Rudge, Timothy

2017-01-01

The advent of easy-to-use open source microcontrollers, off-the-shelf electronics and customizable manufacturing technologies has facilitated the development of inexpensive scientific devices and laboratory equipment. In this study, we describe an imaging system that integrates low-cost and open-source hardware, software and genetic resources. The multi-fluorescence imaging system consists of readily available 470 nm LEDs, a Raspberry Pi camera and a set of filters made with low cost acrylics. This device allows imaging in scales ranging from single colonies to entire plates. We developed a set of genetic components (e.g. promoters, coding sequences, terminators) and vectors following the standard framework of Golden Gate, which allowed the fabrication of genetic constructs in a combinatorial, low cost and robust manner. In order to provide simultaneous imaging of multiple wavelength signals, we screened a series of long stokes shift fluorescent proteins that could be combined with cyan/green fluorescent proteins. We found CyOFP1, mBeRFP and sfGFP to be the most compatible set for 3-channel fluorescent imaging. We developed open source Python code to operate the hardware to run time-lapse experiments with automated control of illumination and camera and a Python module to analyze data and extract meaningful biological information. To demonstrate the potential application of this integral system, we tested its performance on a diverse range of imaging assays often used in disciplines such as microbial ecology, microbiology and synthetic biology. We also assessed its potential use in a high school environment to teach biology, hardware design, optics, and programming. Together, these results demonstrate the successful integration of open source hardware, software, genetic resources and customizable manufacturing to obtain a powerful, low cost and robust system for education, scientific research and bioengineering. All the resources developed here are available under open source licenses. PMID:29140977

Genetic variability in krill.

PubMed

Valentine, J W; Ayala, F J

1976-02-01

We have estimated genetic variability by gel electrophoresis in three species of krill, genus Euphausia (Arthropoda: Crustacea). Genetic variability is low where trophic resources are most seasonal, and high where trophic resources are most stable. Simlar trends have been found in benthic marine invertebrates. The observed trends of genetic variability do not correlate with trends in the stability of physical environment parameters.

Strategies for conserving forest genetic resources in the face of climate change

Treesearch

John Bradley St. Clair; Glenn Thomas Howe

2011-01-01

Conservation of genetic diversity is important for continued evolution of populations to new environments, as well as continued availability of traits of interest in genetic improvement programs. Rapidly changing climates present new threats to the conservation of forest genetic resources. We can no longer assume that in situ reserves will continue to preserve existing...

[Public health, genetics and ethics].

PubMed

Kottow, Miguel H

2002-10-01

Genetics research has shown enormous developments in recent decades, although as yet with only limited clinical application. Bioethical analysis has been unable to deal with the vast problems of genetics because emphasis has been put on the principlism applied to both clinical and research bioethics. Genetics nevertheless poses its most complex moral dilemmas at the public level, where a social brand of ethics ought to supersede the essentially interpersonal perspective of principlism. A more social understanding of ethics in genetics is required to unravel issues such as research and clinical explorations, ownership and patents, genetic manipulation, and allocation of resources. All these issues require reflection based on the requirements of citizenry, consideration of common assets, and definition of public policies in regulating genetic endeavors and protecting the society as a whole Bioethics has privileged the approach to individual ethical issues derived from genetic intervention, thereby neglecting the more salient aspects of genetics and social ethics.

Genetic counselling in the era of genomic medicine

PubMed Central

Middleton, Anna

2018-01-01

Abstract Background Genomic technology can now deliver cost effective, targeted diagnosis and treatment for patients. Genetic counselling is a communication process empowering patients and families to make autonomous decisions and effectively use new genetic information. The skills of genetic counselling and expertise of genetic counsellors are integral to the effective implementation of genomic medicine. Sources of data Original papers, reviews, guidelines, policy papers and web-resources. Areas of agreement An international consensus on the definition of genetic counselling. Genetic counselling is necessary for implementation of genomic medicine. Areas of controversy Models of genetic counselling. Growing points Genomic medicine is a growing and strategic priority for many health care systems. Genetic counselling is part of this. Areas timely for developing research An evidence base is necessary, incorporating implementation and outcome research, to enable health care systems, practitioners, patients and families to maximize the utility (medically and psychologically) of the new genomic possibilities. PMID:29617718

Genetics Home Reference: 48,XXYY syndrome

MedlinePlus

... degree of difficulty with speech and language development. Learning disabilities, especially those that are language-based, are very ... Autism Speaks CHADD: The National Resource on ADHD Learning Disabilities Association of America National Center for Learning Disabilities ...

Fine-Scale Ecological and Genetic Population Structure of Two Whitefish (Coregoninae) Species in the Vicinity of Industrial Thermal Emissions.

PubMed

Graham, Carly F; Eberts, Rebecca L; Morgan, Thomas D; Boreham, Douglas R; Lance, Stacey L; Manzon, Richard G; Martino, Jessica A; Rogers, Sean M; Wilson, Joanna Y; Somers, Christopher M

2016-01-01

Thermal pollution from industrial processes can have negative impacts on the spawning and development of cold-water fish. Point sources of thermal effluent may need to be managed to avoid affecting discrete populations. Correspondingly, we examined fine-scale ecological and genetic population structure of two whitefish species (Coregonus clupeaformis and Prosopium cylindraceum) on Lake Huron, Canada, in the immediate vicinity of thermal effluent from nuclear power generation. Niche metrics using δ13C and δ15N stable isotopes showed high levels of overlap (48.6 to 94.5%) in resource use by adult fish captured in areas affected by thermal effluent compared to nearby reference locations. Isotopic niche size, a metric of resource use diversity, was 1.3- to 2.8-fold higher than reference values in some thermally affected areas, indicative of fish mixing. Microsatellite analyses of genetic population structure (Fst, STRUCTURE and DAPC) indicated that fish captured at all locations in the vicinity of the power plant were part of a larger population extending beyond the study area. In concert, ecological and genetic markers do not support the presence of an evolutionarily significant unit in the vicinity of the power plant. Thus, future research should focus on the potential impacts of thermal emissions on development and recruitment.

Fine-Scale Ecological and Genetic Population Structure of Two Whitefish (Coregoninae) Species in the Vicinity of Industrial Thermal Emissions

PubMed Central

Graham, Carly F.; Eberts, Rebecca L.; Morgan, Thomas D.; Boreham, Douglas R.; Lance, Stacey L.; Manzon, Richard G.; Martino, Jessica A.; Rogers, Sean M.; Wilson, Joanna Y.; Somers, Christopher M.

2016-01-01

Thermal pollution from industrial processes can have negative impacts on the spawning and development of cold-water fish. Point sources of thermal effluent may need to be managed to avoid affecting discrete populations. Correspondingly, we examined fine-scale ecological and genetic population structure of two whitefish species (Coregonus clupeaformis and Prosopium cylindraceum) on Lake Huron, Canada, in the immediate vicinity of thermal effluent from nuclear power generation. Niche metrics using δ13C and δ15N stable isotopes showed high levels of overlap (48.6 to 94.5%) in resource use by adult fish captured in areas affected by thermal effluent compared to nearby reference locations. Isotopic niche size, a metric of resource use diversity, was 1.3- to 2.8-fold higher than reference values in some thermally affected areas, indicative of fish mixing. Microsatellite analyses of genetic population structure (Fst, STRUCTURE and DAPC) indicated that fish captured at all locations in the vicinity of the power plant were part of a larger population extending beyond the study area. In concert, ecological and genetic markers do not support the presence of an evolutionarily significant unit in the vicinity of the power plant. Thus, future research should focus on the potential impacts of thermal emissions on development and recruitment. PMID:26807722

Developing education tailored to clinical roles: genetics education for haemophilia nurses.

PubMed

Burke, Sarah; Barker, Colin; Marshall, Dianne

2012-01-01

Genetics is an important component of the clinical work of haemophilia nurses, but little was known about the genetic education needs of haemophilia nurses. To develop, deliver and evaluate genetic education for haemophilia nurses, based on clinical roles. Perceived relevance of genetics to haemophilia nursing practice was explored using electronic voting (response rate 75%, 58/77). A follow-on questionnaire to a volunteer sample of participants explored educational preferences (response rate 41%, 17/41). Results informed development of a two-hour genetics workshop session, evaluated by questionnaire (response rate 67%, 47/70). Genetic competences were considered relevant to the clinical practice of haemophilia nurses, and learning needs were identified. Preference was expressed for education focused on practical skills. During the subsequent workshop, participant confidence ratings significantly increased in the four areas addressed. Planned changes to clinical care and training were reported. Within new areas of advanced nursing practice, learning needs can be addressed by: identifying relevant clinical activities and associated learning needs; creating a strategy and resources using preferred forms of delivery; implementing the strategy; and evaluating its effect. This will enable development of education that addresses the real needs of practising nurses, grounded in their daily clinical practice. Copyright © 2011 Elsevier Ltd. All rights reserved.

Genetic Distinctiveness of Rye In situ Accessions from Portugal Unveils a New Hotspot of Unexplored Genetic Resources

PubMed Central

Monteiro, Filipa; Vidigal, Patrícia; Barros, André B.; Monteiro, Ana; Oliveira, Hugo R.; Viegas, Wanda

2016-01-01

Rye (Secale cereale L.) is a cereal crop of major importance in many parts of Europe and rye breeders are presently very concerned with the restrict pool of rye genetic resources available. Such narrowing of rye genetic diversity results from the presence of “Petkus” pool in most modern rye varieties as well as “Petkus” × “Carsten” heterotic pool in hybrid rye breeding programs. Previous studies on rye's genetic diversity revealed moreover a common genetic background on landraces (ex situ) and cultivars, regardless of breeding level or geographical origin. Thus evaluation of in situ populations is of utmost importance to unveil “on farm” diversity, which is largely undervalued. Here, we perform the first comprehensive assessment of rye's genetic diversity and population structuring using cultivars, ex situ landraces along a comprehensive sampling of in situ accessions from Portugal, through a molecular-directed analysis using SSRs markers. Rye genetic diversity and population structure analysis does not present any geographical trend but disclosed marked differences between genetic backgrounds of in situ accessions and those of cultivars/ex situ collections. Such genetic distinctiveness of in situ accessions highlights their unexplored potential as new genetic resources, which can be used to boost rye breeding strategies and the production of new varieties. Overall, our study successfully demonstrates the high prospective impact of comparing genetic diversity and structure of cultivars, ex situ, and in situ samples in ascertaining the status of plant genetic resources (PGR). PMID:27630658

Genetic diversity revealed by single nucleotide polymorphism markers in a worldwide germplasm collection of durum wheat.

PubMed

Ren, Jing; Sun, Daokun; Chen, Liang; You, Frank M; Wang, Jirui; Peng, Yunliang; Nevo, Eviatar; Sun, Dongfa; Luo, Ming-Cheng; Peng, Junhua

2013-03-28

Evaluation of genetic diversity and genetic structure in crops has important implications for plant breeding programs and the conservation of genetic resources. Newly developed single nucleotide polymorphism (SNP) markers are effective in detecting genetic diversity. In the present study, a worldwide durum wheat collection consisting of 150 accessions was used. Genetic diversity and genetic structure were investigated using 946 polymorphic SNP markers covering the whole genome of tetraploid wheat. Genetic structure was greatly impacted by multiple factors, such as environmental conditions, breeding methods reflected by release periods of varieties, and gene flows via human activities. A loss of genetic diversity was observed from landraces and old cultivars to the modern cultivars released during periods of the Early Green Revolution, but an increase in cultivars released during the Post Green Revolution. Furthermore, a comparative analysis of genetic diversity among the 10 mega ecogeographical regions indicated that South America, North America, and Europe possessed the richest genetic variability, while the Middle East showed moderate levels of genetic diversity.

The development and phenotyping of diploid recombinant inbred lines of potato

USDA-ARS?s Scientific Manuscript database

Progress continues to be made in the effort to transform potato from a tetraploid outbreeding crop into a diploid inbreeding one. This transformation will ultimately lead to more efficient breeding and cultivar development. A variety of genetic resources will be required before a cultivated diploid ...

Dedication: Major M. Goodman, Maize Breeder and Geneticist

USDA-ARS?s Scientific Manuscript database

Major M. Goodman is the leading expert on the classification and use of the diverse genetic resources of maize. He pioneered the development and use of mathematical approaches to classification of diverse plant materials; had a primary role in the development of one of the first comprehensive plant ...

The GRIN-Global Information Management System – A Preview and Opportunity for Public User Input

USDA-ARS?s Scientific Manuscript database

The GRIN-Global Information Management System, under development for the past two years, will provide the world's crop genebanks and plant genetic resource (PGR) users with a powerful, flexible, easy-to-use PGR information management system. Developed jointly by the USDA Agricultural Research Servi...

The GRIN-Global Information Management System – Public Interface Demonstration and Input Opportunity

USDA-ARS?s Scientific Manuscript database

The GRIN-Global (GG) Information Management System, under development for the past three years, provides the world's crop genebanks and plant genetic resource (PGR) users with a powerful, flexible, easy-to-use PGR information management system. Developed jointly by the USDA Agricultural Research Ser...

Harvesting Legume Genomes: Plant Genetic Resources

USDA-ARS?s Scientific Manuscript database

Genomics and high through-put phenotyping are ushering in a new era of accessing genetic diversity held in plant genetic resources, the cornerstone of both traditional and genomics-assisted breeding efforts of food legume crops. Acknowledged or not, yield plateaus must be broken given the daunting ...

Antagonistic interactions peak at intermediate genetic distance in clinical and laboratory strains of Pseudomonas aeruginosa.

PubMed

Schoustra, Sijmen E; Dench, Jonathan; Dali, Rola; Aaron, Shawn D; Kassen, Rees

2012-03-22

Bacteria excrete costly toxins to defend their ecological niche. The evolution of such antagonistic interactions between individuals is expected to depend on both the social environment and the strength of resource competition. Antagonism is expected to be weak among highly similar genotypes because most individuals are immune to antagonistic agents and among dissimilar genotypes because these are unlikely to be competing for the same resources and antagonism should not yield much benefit. The strength of antagonism is therefore expected to peak at intermediate genetic distance. We studied the ability of laboratory strains of Pseudomonas aeruginosa to prevent growth of 55 different clinical P. aeruginosa isolates derived from cystic fibrosis patients. Genetic distance was determined using genetic fingerprints. We found that the strength of antagonism was maximal among genotypes of intermediate genetic distance and we show that genetic distance and resource use are linked. Our results suggest that the importance of social interactions like antagonism may be modulated by the strength of resource competition.

Genetic variability in krill.

PubMed Central

Valentine, J W; Ayala, F J

1976-01-01

We have estimated genetic variability by gel electrophoresis in three species of krill, genus Euphausia (Arthropoda: Crustacea). Genetic variability is low where trophic resources are most seasonal, and high where trophic resources are most stable. Simlar trends have been found in benthic marine invertebrates. The observed trends of genetic variability do not correlate with trends in the stability of physical environment parameters. Images PMID:1061166

Integration of population genetic structure and plant response to climate change: sustaining genetic resources through evaluation of projected threats

Treesearch

Bryce A. Richardson; Marcus V. Warwell; Mee-Sook Kim; Ned B. Klopfenstein; Geral I. McDonald

2010-01-01

To assess threats or predict responses to disturbances, or both, it is essential to recognize and characterize the population structures of forest species in relation to changing environments. Appropriate management of these genetic resources in the future will require (1) understanding the existing genetic diversity/variation and population structure of forest trees...

Phenome-Wide Association Studies as a Tool to Advance Precision Medicine

PubMed Central

Denny, Joshua C.; Bastarache, Lisa; Roden, Dan M.

2017-01-01

Beginning in the early 2000s, the accumulation of biospecimens linked to electronic health records (EHRs) made possible genome-phenome studies (i.e., comparative analyses of genetic variants and phenotypes) using only data collected as a by-product of typical health care. In addition to disease and trait genetics, EHRs proved a valuable resource for analyzing pharmacogenetic traits and developing reverse genetics approaches such as phenome-wide association studies (PheWASs). PheWASs are designed to survey which of many phenotypes may be associated with a given genetic variant. PheWAS methods have been validated through replication of hundreds of known genotype-phenotype associations, and their use has differentiated between true pleiotropy and clinical comorbidity, added context to genetic discoveries, and helped define disease subtypes, and may also help repurpose medications. PheWAS methods have also proven to be useful with research-collected data. Future efforts that integrate broad, robust collection of phenotype data (e.g., EHR data) with purpose-collected research data in combination with a greater understanding of EHR data will create a rich resource for increasingly more efficient and detailed genome-phenome analysis to usher in new discoveries in precision medicine. PMID:27147087

Climbing the Ladder: Experience with Developing a Large Group Genetic Counselor Career Ladder at Children's National Health System.

PubMed

Kofman, Laura; Seprish, Mary Beth; Summar, Marshall

2016-08-01

Children's National Health System (CNHS) is a not-for-profit pediatric hospital that employs around twenty genetic counselors in a range of specialties, including clinical pediatric, neurology, fetal medicine, research, and laboratory. CNHS lacked a structured system of advancement for their genetic counselors; therefore, a formal career ladder was proposed by the genetic counselors based on years of experience, responsibility, and job performance. This career ladder utilized monetary, academic, and seniority incentives to encourage advancement and continue employment at CNHS. The creation and ultimate approval of the career ladder required direct input from genetic counselors, Department Chairs, and Human Resource personnel. The establishment of a genetic counselor career ladder at CNHS will hopefully benefit the profession of genetic counselors as a whole and allow other facilities to create and maintain their own career ladder to meet the needs of the growing, competitive, field of genetic counseling.

Mutagenesis and phenotyping resources in zebrafish for studying development and human disease

PubMed Central

Varshney, Gaurav Kumar

2014-01-01

The zebrafish (Danio rerio) is an important model organism for studying development and human disease. The zebrafish has an excellent reference genome and the functions of hundreds of genes have been tested using both forward and reverse genetic approaches. Recent years have seen an increasing number of large-scale mutagenesis projects and the number of mutants or gene knockouts in zebrafish has increased rapidly, including for the first time conditional knockout technologies. In addition, targeted mutagenesis techniques such as zinc finger nucleases, transcription activator-like effector nucleases and clustered regularly interspaced short sequences (CRISPR) or CRISPR-associated (Cas), have all been shown to effectively target zebrafish genes as well as the first reported germline homologous recombination, further expanding the utility and power of zebrafish genetics. Given this explosion of mutagenesis resources, it is now possible to perform systematic, high-throughput phenotype analysis of all zebrafish gene knockouts. PMID:24162064

Developing a typology for local cattle breed farmers in Europe.

PubMed

Soini, K; Diaz, C; Gandini, G; de Haas, Y; Lilja, T; Martin-Collado, D; Pizzi, F; Hiemstra, S J

2012-12-01

Recognizing cultural diversity among local breed farmers is crucial for the successful development and implementation of farm animal genetic resources FAnGr conservation policies and programmes. In this study based on survey data collected in the EUropean REgional CAttle breeds project from six European countries, a typology of local breed farmers was designed and profiles for each of the farmer types were developed to assist these policy needs. Three main farmer types were constructed: production-oriented, product and service-oriented and hobby-oriented farmers. In addition, seven subtypes were characterized under the main types: sustainable producers, opportunists, multi-users, brand makers, traditionalists, pragmatists and newcomers. These types have many similarities to the 'productivist', 'multifunctional' and 'post-productivist' farmer types. The typology not only reveals the high level of diversity among local cattle breed farmers in Europe, which presents an opportunity for the in situ conservation of animal genetic resources, but also a challenge for policy to meet the differing requirements of the farmer types. © 2012 Blackwell Verlag GmbH.

Resources for Biological Annotation of the Drosophila Genome

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gerald M. Rubin

2005-08-08

This project supported seed money for the development of cDNA and genetic resources to support studies of the Drosophila melanogaster genome. Key publications supported by this work that provide additional detail: (1) ''The Drosophila gene collection: identification of putative full-length cDNAs for 70% of D. melanogaster genes''; and (2) ''The Berkeley Drosophila Genome Project gene disruption project: Single P-element insertions mutating 25% of vital Drosophila genes''.

Coordination and collaboration to document the global cotton germplasm resources

USDA-ARS?s Scientific Manuscript database

Coordinated efforts to collect and maintain cotton genetic resources have increased over the last 100 years to insure the worldwide economic value of cotton fiber and cotton byproducts. The classified genetic resources of cotton are extensive and include five tetraploid species in the primary gene ...

Protocol for investigating genetic determinants of posttraumatic stress disorder in women from the Nurses' Health Study II

PubMed Central

Koenen, Karestan C; DeVivo, Immaculata; Rich-Edwards, Janet; Smoller, Jordan W; Wright, Rosalind J; Purcell, Shaun M

2009-01-01

Background One in nine American women will meet criteria for the diagnosis of posttraumatic stress disorder (PTSD) in their lifetime. Although twin studies suggest genetic influences account for substantial variance in PTSD risk, little progress has been made in identifying variants in specific genes that influence liability to this common, debilitating disorder. Methods and design We are using the unique resource of the Nurses Health Study II, a prospective epidemiologic cohort of 68,518 women, to conduct what promises to be the largest candidate gene association study of PTSD to date. The entire cohort will be screened for trauma exposure and PTSD; 3,000 women will be selected for PTSD diagnostic interviews based on the screening data. Our nested case-control study will genotype1000 women who developed PTSD following a history of trauma exposure; 1000 controls will be selected from women who experienced similar traumas but did not develop PTSD. The primary aim of this study is to detect genetic variants that predict the development of PTSD following trauma. We posit inherited vulnerability to PTSD is mediated by genetic variation in three specific neurobiological systems whose alterations are implicated in PTSD etiology: the hypothalamic-pituitary-adrenal axis, the locus coeruleus/noradrenergic system, and the limbic-frontal neuro-circuitry of fear. The secondary, exploratory aim of this study is to dissect genetic influences on PTSD in the broader genetic and environmental context for the candidate genes that show significant association with PTSD in detection analyses. This will involve: conducting conditional tests to identify the causal genetic variant among multiple correlated signals; testing whether the effect of PTSD genetic risk variants is moderated by age of first trauma, trauma type, and trauma severity; and exploring gene-gene interactions using a novel gene-based statistical approach. Discussion Identification of liability genes for PTSD would represent a major advance in understanding the pathophysiology of the disorder. Such understanding could advance the development of new pharmacological agents for PTSD treatment and prevention. Moreover, the addition of PTSD assessment data will make the NHSII cohort an unparalleled resource for future genetic studies of PTSD as well as provide the unique opportunity for the prospective examination of PTSD-disease associations. PMID:19480706

Advances in Genetical Genomics of Plants

PubMed Central

Joosen, R.V.L.; Ligterink, W.; Hilhorst, H.W.M.; Keurentjes, J.J.B.

2009-01-01

Natural variation provides a valuable resource to study the genetic regulation of quantitative traits. In quantitative trait locus (QTL) analyses this variation, captured in segregating mapping populations, is used to identify the genomic regions affecting these traits. The identification of the causal genes underlying QTLs is a major challenge for which the detection of gene expression differences is of major importance. By combining genetics with large scale expression profiling (i.e. genetical genomics), resulting in expression QTLs (eQTLs), great progress can be made in connecting phenotypic variation to genotypic diversity. In this review we discuss examples from human, mouse, Drosophila, yeast and plant research to illustrate the advances in genetical genomics, with a focus on understanding the regulatory mechanisms underlying natural variation. With their tolerance to inbreeding, short generation time and ease to generate large families, plants are ideal subjects to test new concepts in genetics. The comprehensive resources which are available for Arabidopsis make it a favorite model plant but genetical genomics also found its way to important crop species like rice, barley and wheat. We discuss eQTL profiling with respect to cis and trans regulation and show how combined studies with other ‘omics’ technologies, such as metabolomics and proteomics may further augment current information on transcriptional, translational and metabolomic signaling pathways and enable reconstruction of detailed regulatory networks. The fast developments in the ‘omics’ area will offer great potential for genetical genomics to elucidate the genotype-phenotype relationships for both fundamental and applied research. PMID:20514216

Communication of Psychiatric Risk in 22q11.2 Deletion Syndrome: A Pilot Project.

PubMed

Hart, Sarah J; Schoch, Kelly; Shashi, Vandana; Callanan, Nancy

2016-02-01

Individuals with 22q11.2 deletion syndrome (22q11.2DS) have an increased chance of developing a psychiatric disorder. While parents of children affected by 22q11.2DS typically receive counseling about risk for non-psychiatric health concerns, genetic counselors may be reluctant to discuss psychiatric risk. Further education of genetic counselors may be necessary to encourage discussion of psychiatric risk with these families. The goal of this project was to develop recommendations for genetic counselors to provide psychiatric risk information to families affected by 22q11.2DS. The recommendations were developed by synthesizing resources in the literature about risk communication. These recommendations were refined following an online focus group meeting with five health care professionals who were recruited for participation from 22q11.2DS clinics across the U.S.A. The focus group data revealed three themes related to discussion of psychiatric risk: 1) Stepwise approach, 2) Discussing treatment options and reducing risks, and 3) Addressing stigma. These recommendations may be used as a foundation for a future clinical protocol to encourage discussion about the risk for psychiatric illness at an earlier point in the diagnostic process for 22q11.2DS and to provide improved information, support and resources to affected families.

Resource Allocation in a Repetitive Project Scheduling Using Genetic Algorithm

NASA Astrophysics Data System (ADS)

Samuel, Biju; Mathew, Jeeno

2018-03-01

Resource Allocation is procedure of doling out or allocating the accessible assets in a monetary way and productive way. Resource allocation is the scheduling of the accessible assets and accessible exercises or activities required while thinking about both the asset accessibility and the total project completion time. Asset provisioning and allocation takes care of that issue by permitting the specialist co-ops to deal with the assets for every individual demand of asset. A probabilistic selection procedure has been developed in order to ensure various selections of chromosomes

Scaling up: human genetics as a Cold War network.

PubMed

Lindee, Susan

2014-09-01

In this commentary I explore how the papers here illuminate the processes of collection that have been so central to the history of human genetics since 1945. The development of human population genetics in the Cold War period produced databases and biobanks that have endured into the present, and that continue to be used and debated. In the decades after the bomb, scientists collected and transferred human biological materials and information from populations of interest, and as they moved these biological resources or biosocial resources acquired new meanings and uses. The papers here collate these practices and map their desires and ironies. They explore how a large international network of geneticists, biological anthropologists, virologists and other physicians and scientists interacted with local informants, research subjects and public officials. They also track the networks and standards that mobilized the transfer of information, genealogies, tissue and blood samples. As Joanna Radin suggests here, the massive collections of human biological materials and data were often understood to be resources for an "as-yet-unknown" future. The stories told here contain elements of surveillance, extraction, salvage and eschatology. Copyright © 2014 Elsevier Ltd. All rights reserved.

A methodological approach to identify agro-biodiversity hotspots for priority in situ conservation of plant genetic resources

PubMed Central

Pacicco, Luca; Bodesmo, Mara; Torricelli, Renzo

2018-01-01

Agro-biodiversity is seriously threatened worldwide and strategies to preserve it are dramatically required. We propose here a methodological approach aimed to identify areas with a high level of agro-biodiversity in which to set or enhance in situ conservation of plant genetic resources. These areas are identified using three criteria: Presence of Landrace diversity, Presence of wild species and Agro-ecosystem ecological diversity. A Restrictive and an Additive prioritization strategy has been applied on the entire Italian territory and has resulted in establishing nationwide 53 and 197 agro-biodiversity hotspots respectively. At present the strategies can easily be applied at a European level and can be helpful to develop conservation strategies everywhere. PMID:29856765

Development of Genetic Occurrence Models for Geothermal Prospecting

NASA Astrophysics Data System (ADS)

Walker, J. D.; Sabin, A.; Unruh, J.; Monastero, F. C.; Combs, J.

2007-12-01

Exploration for utility-grade geothermal resources has mostly relied on identifying obvious surface manifestations of possible geothermal activity, e.g., locating and working near steaming ground or hot springs. This approach has lead to the development of over 130 resources worldwide, but geothermal exploration done in this manner is akin to locating hydrocarbon plays by searching for oil seeps. Confining exploration to areas with such features will clearly not discover a blind resource, that is, one that does not have surface expression. Blind resources, however, constitute the vast majority of hydrocarbon plays; this may be the case for geothermal resources as well. We propose a geothermal exploration strategy for finding blind systems that is based on an understanding of the geologic processes that transfer heat from the mantle to the upper crust and foster the conditions for hydrothermal circulation or enhanced geothermal exploration. The strategy employs a genetically based screening protocol to assess potential geothermal sites. The approach starts at the plate boundary scale and progressively focuses in on the scale of a producing electrical-grade field. Any active margin or hot spot is a potential location for geothermal resources. Although Quaternary igneous activity provides a clear indication of active advection of hot material into the upper crust, it is not sufficient to guarantee a potential utility-grade resource. Active faulting and/or evidence of high strain rates appear to be the critical features associated with areas of utility-grade geothermal potential. This is because deformation on its own can advect sufficient heat into the upper crust to create conditions favorable for geothermal exploitation. In addition, active deformation is required to demonstrate that open pathways for circulation of geothermal fluids are present and/or can be maintained. The last step in the screening protocol is to identify any evidence of geothermal activity, including high heat flow, anomalous temperature water wells, high-temperature indications from aqueous geothermometry and geochemistry, Pliocene or younger ages from low-temperature thermochronometers, as well as more obvious factors such as geysers and fumaroles (which by definition will be missing for blind resources). Our occurrence-model strategy inverts the current approach that relies first on obvious evidence of geothermal activity. We evaluated our approach by retrospectively applying the protocol to the characteristics of producing geothermal fields, and in all cases, known resource areas fit the parameters identified from a genetic perspective.

Construction of the first genetic linkage map of Japanese gentian (Gentianaceae)

PubMed Central

2012-01-01

Background Japanese gentians (Gentiana triflora and Gentiana scabra) are amongst the most popular floricultural plants in Japan. However, genomic resources for Japanese gentians have not yet been developed, mainly because of the heterozygous genome structure conserved by outcrossing, the long juvenile period, and limited knowledge about the inheritance of important traits. In this study, we developed a genetic linkage map to improve breeding programs of Japanese gentians. Results Enriched simple sequence repeat (SSR) libraries from a G. triflora double haploid line yielded almost 20,000 clones using 454 pyrosequencing technology, 6.7% of which could be used to design SSR markers. To increase the number of molecular markers, we identified three putative long terminal repeat (LTR) sequences using the recently developed inter-primer binding site (iPBS) method. We also developed retrotransposon microsatellite amplified polymorphism (REMAP) markers combining retrotransposon and inter-simple sequence repeat (ISSR) markers. In addition to SSR and REMAP markers, modified amplified fragment length polymorphism (AFLP) and random amplification polymorphic DNA (RAPD) markers were developed. Using 93 BC1 progeny from G. scabra backcrossed with a G. triflora double haploid line, 19 linkage groups were constructed with a total of 263 markers (97 SSR, 97 AFLP, 39 RAPD, and 30 REMAP markers). One phenotypic trait (stem color) and 10 functional markers related to genes controlling flower color, flowering time and cold tolerance were assigned to the linkage map, confirming its utility. Conclusions This is the first reported genetic linkage map for Japanese gentians and for any species belonging to the family Gentianaceae. As demonstrated by mapping of functional markers and the stem color trait, our results will help to explain the genetic basis of agronomic important traits, and will be useful for marker-assisted selection in gentian breeding programs. Our map will also be an important resource for further genetic analyses such as mapping of quantitative trait loci and map-based cloning of genes in this species. PMID:23186361

Aquaculture genomics, genetics and breeding in the United States: current status, challenges, and priorities for future research.

PubMed

Abdelrahman, Hisham; ElHady, Mohamed; Alcivar-Warren, Acacia; Allen, Standish; Al-Tobasei, Rafet; Bao, Lisui; Beck, Ben; Blackburn, Harvey; Bosworth, Brian; Buchanan, John; Chappell, Jesse; Daniels, William; Dong, Sheng; Dunham, Rex; Durland, Evan; Elaswad, Ahmed; Gomez-Chiarri, Marta; Gosh, Kamal; Guo, Ximing; Hackett, Perry; Hanson, Terry; Hedgecock, Dennis; Howard, Tiffany; Holland, Leigh; Jackson, Molly; Jin, Yulin; Khalil, Karim; Kocher, Thomas; Leeds, Tim; Li, Ning; Lindsey, Lauren; Liu, Shikai; Liu, Zhanjiang; Martin, Kyle; Novriadi, Romi; Odin, Ramjie; Palti, Yniv; Peatman, Eric; Proestou, Dina; Qin, Guyu; Reading, Benjamin; Rexroad, Caird; Roberts, Steven; Salem, Mohamed; Severin, Andrew; Shi, Huitong; Shoemaker, Craig; Stiles, Sheila; Tan, Suxu; Tang, Kathy F J; Thongda, Wilawan; Tiersch, Terrence; Tomasso, Joseph; Prabowo, Wendy Tri; Vallejo, Roger; van der Steen, Hein; Vo, Khoi; Waldbieser, Geoff; Wang, Hanping; Wang, Xiaozhu; Xiang, Jianhai; Yang, Yujia; Yant, Roger; Yuan, Zihao; Zeng, Qifan; Zhou, Tao

2017-02-20

Advancing the production efficiency and profitability of aquaculture is dependent upon the ability to utilize a diverse array of genetic resources. The ultimate goals of aquaculture genomics, genetics and breeding research are to enhance aquaculture production efficiency, sustainability, product quality, and profitability in support of the commercial sector and for the benefit of consumers. In order to achieve these goals, it is important to understand the genomic structure and organization of aquaculture species, and their genomic and phenomic variations, as well as the genetic basis of traits and their interrelationships. In addition, it is also important to understand the mechanisms of regulation and evolutionary conservation at the levels of genome, transcriptome, proteome, epigenome, and systems biology. With genomic information and information between the genomes and phenomes, technologies for marker/causal mutation-assisted selection, genome selection, and genome editing can be developed for applications in aquaculture. A set of genomic tools and resources must be made available including reference genome sequences and their annotations (including coding and non-coding regulatory elements), genome-wide polymorphic markers, efficient genotyping platforms, high-density and high-resolution linkage maps, and transcriptome resources including non-coding transcripts. Genomic and genetic control of important performance and production traits, such as disease resistance, feed conversion efficiency, growth rate, processing yield, behaviour, reproductive characteristics, and tolerance to environmental stressors like low dissolved oxygen, high or low water temperature and salinity, must be understood. QTL need to be identified, validated across strains, lines and populations, and their mechanisms of control understood. Causal gene(s) need to be identified. Genetic and epigenetic regulation of important aquaculture traits need to be determined, and technologies for marker-assisted selection, causal gene/mutation-assisted selection, genome selection, and genome editing using CRISPR and other technologies must be developed, demonstrated with applicability, and application to aquaculture industries.Major progress has been made in aquaculture genomics for dozens of fish and shellfish species including the development of genetic linkage maps, physical maps, microarrays, single nucleotide polymorphism (SNP) arrays, transcriptome databases and various stages of genome reference sequences. This paper provides a general review of the current status, challenges and future research needs of aquaculture genomics, genetics, and breeding, with a focus on major aquaculture species in the United States: catfish, rainbow trout, Atlantic salmon, tilapia, striped bass, oysters, and shrimp. While the overall research priorities and the practical goals are similar across various aquaculture species, the current status in each species should dictate the next priority areas within the species. This paper is an output of the USDA Workshop for Aquaculture Genomics, Genetics, and Breeding held in late March 2016 in Auburn, Alabama, with participants from all parts of the United States.

Genomics-assisted breeding in four major pulse crops of developing countries: present status and prospects.

PubMed

Bohra, Abhishek; Pandey, Manish K; Jha, Uday C; Singh, Balwant; Singh, Indra P; Datta, Dibendu; Chaturvedi, Sushil K; Nadarajan, N; Varshney, Rajeev K

2014-06-01

Given recent advances in pulse molecular biology, genomics-driven breeding has emerged as a promising approach to address the issues of limited genetic gain and low productivity in various pulse crops. The global population is continuously increasing and is expected to reach nine billion by 2050. This huge population pressure will lead to severe shortage of food, natural resources and arable land. Such an alarming situation is most likely to arise in developing countries due to increase in the proportion of people suffering from protein and micronutrient malnutrition. Pulses being a primary and affordable source of proteins and minerals play a key role in alleviating the protein calorie malnutrition, micronutrient deficiencies and other undernourishment-related issues. Additionally, pulses are a vital source of livelihood generation for millions of resource-poor farmers practising agriculture in the semi-arid and sub-tropical regions. Limited success achieved through conventional breeding so far in most of the pulse crops will not be enough to feed the ever increasing population. In this context, genomics-assisted breeding (GAB) holds promise in enhancing the genetic gains. Though pulses have long been considered as orphan crops, recent advances in the area of pulse genomics are noteworthy, e.g. discovery of genome-wide genetic markers, high-throughput genotyping and sequencing platforms, high-density genetic linkage/QTL maps and, more importantly, the availability of whole-genome sequence. With genome sequence in hand, there is a great scope to apply genome-wide methods for trait mapping using association studies and to choose desirable genotypes via genomic selection. It is anticipated that GAB will speed up the progress of genetic improvement of pulses, leading to the rapid development of cultivars with higher yield, enhanced stress tolerance and wider adaptability.

Systematic documentation and analysis of human genetic variation in hemoglobinopathies using the microattribution approach.

PubMed

Giardine, Belinda; Borg, Joseph; Higgs, Douglas R; Peterson, Kenneth R; Philipsen, Sjaak; Maglott, Donna; Singleton, Belinda K; Anstee, David J; Basak, A Nazli; Clark, Barnaby; Costa, Flavia C; Faustino, Paula; Fedosyuk, Halyna; Felice, Alex E; Francina, Alain; Galanello, Renzo; Gallivan, Monica V E; Georgitsi, Marianthi; Gibbons, Richard J; Giordano, Piero C; Harteveld, Cornelis L; Hoyer, James D; Jarvis, Martin; Joly, Philippe; Kanavakis, Emmanuel; Kollia, Panagoula; Menzel, Stephan; Miller, Webb; Moradkhani, Kamran; Old, John; Papachatzopoulou, Adamantia; Papadakis, Manoussos N; Papadopoulos, Petros; Pavlovic, Sonja; Perseu, Lucia; Radmilovic, Milena; Riemer, Cathy; Satta, Stefania; Schrijver, Iris; Stojiljkovic, Maja; Thein, Swee Lay; Traeger-Synodinos, Jan; Tully, Ray; Wada, Takahito; Waye, John S; Wiemann, Claudia; Zukic, Branka; Chui, David H K; Wajcman, Henri; Hardison, Ross C; Patrinos, George P

2011-03-20

We developed a series of interrelated locus-specific databases to store all published and unpublished genetic variation related to hemoglobinopathies and thalassemia and implemented microattribution to encourage submission of unpublished observations of genetic variation to these public repositories. A total of 1,941 unique genetic variants in 37 genes, encoding globins and other erythroid proteins, are currently documented in these databases, with reciprocal attribution of microcitations to data contributors. Our project provides the first example of implementing microattribution to incentivise submission of all known genetic variation in a defined system. It has demonstrably increased the reporting of human variants, leading to a comprehensive online resource for systematically describing human genetic variation in the globin genes and other genes contributing to hemoglobinopathies and thalassemias. The principles established here will serve as a model for other systems and for the analysis of other common and/or complex human genetic diseases.

Genetic engineering of industrial strains of Saccharomyces cerevisiae.

PubMed

Le Borgne, Sylvie

2012-01-01

Genetic engineering has been successfully applied to Saccharomyces cerevisiae laboratory strains for different purposes: extension of substrate range, improvement of productivity and yield, elimination of by-products, improvement of process performance and cellular properties, and extension of product range. The potential of genetically engineered yeasts for the massive production of biofuels as bioethanol and other nonfuel products from renewable resources as lignocellulosic biomass hydrolysates has been recognized. For such applications, robust industrial strains of S. cerevisiae have to be used. Here, some relevant genetic and genomic characteristics of industrial strains are discussed in relation to the problematic of the genetic engineering of such strains. General molecular tools applicable to the manipulation of S. cerevisiae industrial strains are presented and examples of genetically engineered industrial strains developed for the production of bioethanol from lignocellulosic biomass are given.

ETHNOS: A versatile electronic tool for the development and curation of national genetic databases

PubMed Central

2010-01-01

National and ethnic mutation databases (NEMDBs) are emerging online repositories, recording extensive information about the described genetic heterogeneity of an ethnic group or population. These resources facilitate the provision of genetic services and provide a comprehensive list of genomic variations among different populations. As such, they enhance awareness of the various genetic disorders. Here, we describe the features of the ETHNOS software, a simple but versatile tool based on a flat-file database that is specifically designed for the development and curation of NEMDBs. ETHNOS is a freely available software which runs more than half of the NEMDBs currently available. Given the emerging need for NEMDB in genetic testing services and the fact that ETHNOS is the only off-the-shelf software available for NEMDB development and curation, its adoption in subsequent NEMDB development would contribute towards data content uniformity, unlike the diverse contents and quality of the available gene (locus)-specific databases. Finally, we allude to the potential applications of NEMDBs, not only as worldwide central allele frequency repositories, but also, and most importantly, as data warehouses of individual-level genomic data, hence allowing for a comprehensive ethnicity-specific documentation of genomic variation. PMID:20650823

ETHNOS : A versatile electronic tool for the development and curation of national genetic databases.

PubMed

van Baal, Sjozef; Zlotogora, Joël; Lagoumintzis, George; Gkantouna, Vassiliki; Tzimas, Ioannis; Poulas, Konstantinos; Tsakalidis, Athanassios; Romeo, Giovanni; Patrinos, George P

2010-06-01

National and ethnic mutation databases (NEMDBs) are emerging online repositories, recording extensive information about the described genetic heterogeneity of an ethnic group or population. These resources facilitate the provision of genetic services and provide a comprehensive list of genomic variations among different populations. As such, they enhance awareness of the various genetic disorders. Here, we describe the features of the ETHNOS software, a simple but versatile tool based on a flat-file database that is specifically designed for the development and curation of NEMDBs. ETHNOS is a freely available software which runs more than half of the NEMDBs currently available. Given the emerging need for NEMDB in genetic testing services and the fact that ETHNOS is the only off-the-shelf software available for NEMDB development and curation, its adoption in subsequent NEMDB development would contribute towards data content uniformity, unlike the diverse contents and quality of the available gene (locus)-specific databases. Finally, we allude to the potential applications of NEMDBs, not only as worldwide central allele frequency repositories, but also, and most importantly, as data warehouses of individual-level genomic data, hence allowing for a comprehensive ethnicity-specific documentation of genomic variation.

Implementation of genetic conservation practices in a muskellunge propagation and stocking program

USGS Publications Warehouse

Jennings, Martin J.; Sloss, Brian L.; Hatzenbeler, Gene R.; Kampa, Jeffrey M.; Simonson, Timothy D.; Avelallemant, Steven P.; Lindenberger, Gary A.; Underwood, Bruce D.

2010-01-01

Conservation of genetic resources is a challenging issue for agencies managing popular sport fishes. To address the ongoing potential for genetic risks, we developed a comprehensive set of recommendations to conserve genetic diversity of muskellunge (Esox masquinongy) in Wisconsin, and evaluated the extent to which the recommendations can be implemented. Although some details are specific to Wisconsin's muskellunge propagation program, many of the practical issues affecting implementation are applicable to other species and production systems. We developed guidelines to restrict future broodstock collection operations to lakes with natural reproduction and to develop a set of brood lakes to use on a rotational basis within regional stock boundaries, but implementation will require considering lakes with variable stocking histories. Maintaining an effective population size sufficient to minimize the risk of losing alleles requires limiting broodstock collection to large lakes. Recommendations to better approximate the temporal distribution of spawning in hatchery operations and randomize selection of brood fish are feasible. Guidelines to modify rearing and distribution procedures face some logistic constraints. An evaluation of genetic diversity of hatchery-produced fish during 2008 demonstrated variable success representing genetic variation of the source population. Continued evaluation of hatchery operations will optimize operational efficiency while moving toward genetic conservation goals.

Implementation of genetic conservation practices in a muskellunge propagation and stocking program

USGS Publications Warehouse

Jennings, Martin J.; Sloss, Brian L.; Hatzenbeler, Gene R.; Kampa, Jeffrey M.; Simonson, Timothy D.; Avelallemant, Steven P.; Lindenberger, Gary A.; Underwood, Bruce D.

2010-01-01

Conservation of genetic resources is a challenging issue for agencies managing popular sport fishes. To address the ongoing potential for genetic risks, we developed a comprehensive set of recommendations to conserve genetic diversity of muskellunge (Esox masquinongy) in Wisconsin, and evaluated the extent to which the recommendations can be implemented. Although some details are specific to Wisconsin's muskellunge propagation program, many of the practical issues affecting implementation are applicable to other species and production systems. We developed guidelines to restrict future brood stock collection operations to lakes with natural reproduction and to develop a set of brood lakes to use on a rotational basis within regional stock boundaries, but implementation will require considering lakes with variable stocking histories. Maintaining an effective population size sufficient to minimize the risk of losing alleles requires limiting brood stock collection to large lakes. Recommendations to better approximate the temporal distribution of spawning in hatchery operations and randomize selection of brood fish are feasible. Guidelines to modify rearing and distribution procedures face some logistic constraints. An evaluation of genetic diversity of hatchery-produced fish during 2008 demonstrated variable success representing genetic variation of the source population. Continued evaluation of hatchery operations will optimize operational efficiency while moving toward genetic conservation goals.

How Are Genetic Conditions Diagnosed?

MedlinePlus

... Consultation How are genetic conditions diagnosed? How are genetic conditions diagnosed? A doctor may suspect a diagnosis ... and advocacy resources. For more information about diagnosing genetic conditions: Genetics Home Reference provides information about genetic ...

Gramene 2013: comparative plant genomics resources.

PubMed

Monaco, Marcela K; Stein, Joshua; Naithani, Sushma; Wei, Sharon; Dharmawardhana, Palitha; Kumari, Sunita; Amarasinghe, Vindhya; Youens-Clark, Ken; Thomason, James; Preece, Justin; Pasternak, Shiran; Olson, Andrew; Jiao, Yinping; Lu, Zhenyuan; Bolser, Dan; Kerhornou, Arnaud; Staines, Dan; Walts, Brandon; Wu, Guanming; D'Eustachio, Peter; Haw, Robin; Croft, David; Kersey, Paul J; Stein, Lincoln; Jaiswal, Pankaj; Ware, Doreen

2014-01-01

Gramene (http://www.gramene.org) is a curated online resource for comparative functional genomics in crops and model plant species, currently hosting 27 fully and 10 partially sequenced reference genomes in its build number 38. Its strength derives from the application of a phylogenetic framework for genome comparison and the use of ontologies to integrate structural and functional annotation data. Whole-genome alignments complemented by phylogenetic gene family trees help infer syntenic and orthologous relationships. Genetic variation data, sequences and genome mappings available for 10 species, including Arabidopsis, rice and maize, help infer putative variant effects on genes and transcripts. The pathways section also hosts 10 species-specific metabolic pathways databases developed in-house or by our collaborators using Pathway Tools software, which facilitates searches for pathway, reaction and metabolite annotations, and allows analyses of user-defined expression datasets. Recently, we released a Plant Reactome portal featuring 133 curated rice pathways. This portal will be expanded for Arabidopsis, maize and other plant species. We continue to provide genetic and QTL maps and marker datasets developed by crop researchers. The project provides a unique community platform to support scientific research in plant genomics including studies in evolution, genetics, plant breeding, molecular biology, biochemistry and systems biology.

Genetic Testing in Clinical Settings.

PubMed

Franceschini, Nora; Frick, Amber; Kopp, Jeffrey B

2018-04-11

Genetic testing is used for screening, diagnosis, and prognosis of diseases consistent with a genetic cause and to guide drug therapy to improve drug efficacy and avoid adverse effects (pharmacogenomics). This In Practice review aims to inform about DNA-related genetic test availability, interpretation, and recommended clinical actions based on results using evidence from clinical guidelines, when available. We discuss challenges that limit the widespread use of genetic information in the clinical care setting, including a small number of actionable genetic variants with strong evidence of clinical validity and utility, and the need for improving the health literacy of health care providers and the public, including for direct-to-consumer tests. Ethical, legal, and social issues and incidental findings also need to be addressed. Because our understanding of genetic factors associated with disease and drug response is rapidly increasing and new genetic tests are being developed that could be adopted by clinicians in the short term, we also provide extensive resources for information and education on genetic testing. Copyright © 2018 National Kidney Foundation, Inc. All rights reserved.

The Population Reference Sample, POPRES: A Resource for Population, Disease, and Pharmacological Genetics Research

PubMed Central

Nelson, Matthew R.; Bryc, Katarzyna; King, Karen S.; Indap, Amit; Boyko, Adam R.; Novembre, John; Briley, Linda P.; Maruyama, Yuka; Waterworth, Dawn M.; Waeber, Gérard; Vollenweider, Peter; Oksenberg, Jorge R.; Hauser, Stephen L.; Stirnadel, Heide A.; Kooner, Jaspal S.; Chambers, John C.; Jones, Brendan; Mooser, Vincent; Bustamante, Carlos D.; Roses, Allen D.; Burns, Daniel K.; Ehm, Margaret G.; Lai, Eric H.

2008-01-01

Technological and scientific advances, stemming in large part from the Human Genome and HapMap projects, have made large-scale, genome-wide investigations feasible and cost effective. These advances have the potential to dramatically impact drug discovery and development by identifying genetic factors that contribute to variation in disease risk as well as drug pharmacokinetics, treatment efficacy, and adverse drug reactions. In spite of the technological advancements, successful application in biomedical research would be limited without access to suitable sample collections. To facilitate exploratory genetics research, we have assembled a DNA resource from a large number of subjects participating in multiple studies throughout the world. This growing resource was initially genotyped with a commercially available genome-wide 500,000 single-nucleotide polymorphism panel. This project includes nearly 6,000 subjects of African-American, East Asian, South Asian, Mexican, and European origin. Seven informative axes of variation identified via principal-component analysis (PCA) of these data confirm the overall integrity of the data and highlight important features of the genetic structure of diverse populations. The potential value of such extensively genotyped collections is illustrated by selection of genetically matched population controls in a genome-wide analysis of abacavir-associated hypersensitivity reaction. We find that matching based on country of origin, identity-by-state distance, and multidimensional PCA do similarly well to control the type I error rate. The genotype and demographic data from this reference sample are freely available through the NCBI database of Genotypes and Phenotypes (dbGaP). PMID:18760391

Learning about Huntington's Disease

MedlinePlus

... Links for Patient Care Education All About the Human Genome Project Fact Sheets Genetic Education Resources for Teachers ... Education Kit Online Genetics Education Resources Smithsonian NHGRI Genome ... Subjects Research Informed Consent for Genomics Research Intellectual ...

Learning about Myotonic Dystrophy

MedlinePlus

... Links for Patient Care Education All About the Human Genome Project Fact Sheets Genetic Education Resources for Teachers ... Education Kit Online Genetics Education Resources Smithsonian NHGRI Genome ... Subjects Research Informed Consent for Genomics Research Intellectual ...

Fine-scale ecological and genetic population structure of two whitefish (Coregoninae) species in the vicinity of industrial thermal emissions

DOE PAGES

Graham, Carly F.; Eberts, Rebecca L.; Morgan, Thomas D.; ...

2016-01-25

Thermal pollution from industrial processes can have negative impacts on the spawning and development of cold-water fish. Point sources of thermal effluent may need to be managed to avoid affecting discrete populations. Correspondingly, we examined fine-scale ecological and genetic population structure of two whitefish species ( Coregonus clupeaformis and Prosopium cylindraceum) on Lake Huron, Canada, in the immediate vicinity of thermal effluent from nuclear power generation. Niche metrics using δ 13C and δ 15N stable isotopes showed high levels of overlap (48.6 to 94.5%) in resource use by adult fish captured in areas affected by thermal effluent compared to nearbymore » reference locations. Isotopic niche size, a metric of resource use diversity, was 1.3- to 2.8-fold higher than reference values in some thermally affected areas, indicative of fish mixing. Microsatellite analyses of genetic population structure (F st, STRUCTURE and DAPC) indicated that fish captured at all locations in the vicinity of the power plant were part of a larger population extending beyond the study area. In concert, ecological and genetic markers do not support the presence of an evolutionarily significant unit in the vicinity of the power plant. Furthermore, future research should focus on the potential impacts of thermal emissions on development and recruitment.« less

Fine-scale ecological and genetic population structure of two whitefish (Coregoninae) species in the vicinity of industrial thermal emissions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Graham, Carly F.; Eberts, Rebecca L.; Morgan, Thomas D.

Thermal pollution from industrial processes can have negative impacts on the spawning and development of cold-water fish. Point sources of thermal effluent may need to be managed to avoid affecting discrete populations. Correspondingly, we examined fine-scale ecological and genetic population structure of two whitefish species ( Coregonus clupeaformis and Prosopium cylindraceum) on Lake Huron, Canada, in the immediate vicinity of thermal effluent from nuclear power generation. Niche metrics using δ 13C and δ 15N stable isotopes showed high levels of overlap (48.6 to 94.5%) in resource use by adult fish captured in areas affected by thermal effluent compared to nearbymore » reference locations. Isotopic niche size, a metric of resource use diversity, was 1.3- to 2.8-fold higher than reference values in some thermally affected areas, indicative of fish mixing. Microsatellite analyses of genetic population structure (F st, STRUCTURE and DAPC) indicated that fish captured at all locations in the vicinity of the power plant were part of a larger population extending beyond the study area. In concert, ecological and genetic markers do not support the presence of an evolutionarily significant unit in the vicinity of the power plant. Furthermore, future research should focus on the potential impacts of thermal emissions on development and recruitment.« less

Genetic diversity in Carthamus tinctorius (Asteraceae; safflower), an underutilized oilseed crop.

PubMed

Pearl, Stephanie A; Burke, John M

2014-10-01

• Underutilized crops are potentially valuable resources for meeting increasing food demands. Safflower, an oilseed crop, is an example of one such underutilized crop that thrives in moisture-limited areas. Characterization of the genetic diversity maintained within the gene pools of underutilized crops such as safflower is an important step in their further development.• A total of 190 safflower individuals, including 134 USDA accessions, 48 breeding lines from two private North American safflower breeding companies, and eight wild safflower individuals, were genotyped using 133 single nucleotide polymorphism (SNP) markers. We then used the resulting data to assess the amount and distribution of genetic diversity within and among these collections of safflower.• Although just a modest reduction in gene diversity was observed in the commercial breeding lines (relative to the other safflower groupings), safflower domestication was accompanied by a significant decrease in allelic richness. Further, our results suggest that most safflower breeding lines originated from a single pool of diversity within the Old World safflower germplasm.• Taken together, our results suggest that both the safflower germplasm collection and related, wild species harbor previously undocumented genetic diversity that could help fuel future improvement efforts. Paired with analyses of functional diversity, the molecular resources described herein will be thus be useful in the continued development of safflower as an oilseed crop. © 2014 Botanical Society of America, Inc.

Molecular Genetics of Beauveria bassiana Infection of Insects.

PubMed

Ortiz-Urquiza, A; Keyhani, N O

2016-01-01

Research on the insect pathogenic filamentous fungus, Beauveria bassiana has witnessed significant growth in recent years from mainly physiological studies related to its insect biological control potential, to addressing fundamental questions regarding the underlying molecular mechanisms of fungal development and virulence. This has been in part due to a confluence of robust genetic tools and genomic resources for the fungus, and recognition of expanded ecological interactions with which the fungus engages. Beauveria bassiana is a broad host range insect pathogen that has the ability to form intimate symbiotic relationships with plants. Indeed, there is an increasing realization that the latter may be the predominant environmental interaction in which the fungus participates, and that insect parasitism may be an opportunist lifestyle evolved due to the carbon- and nitrogen-rich resources present in insect bodies. Here, we will review progress on the molecular genetics of B. bassiana, which has largely been directed toward identifying genetic pathways involved in stress response and virulence assumed to have practical applications in improving the insect control potential of the fungus. Important strides have also been made in understanding aspects of B. bassiana development. Finally, although increasingly apparent in a number of studies, there is a need for progressing beyond phenotypic mutant characterization to sufficiently investigate the molecular mechanisms underlying B. bassiana's unique and diverse lifestyles as saprophyte, insect pathogen, and plant mutualist. Copyright © 2016 Elsevier Inc. All rights reserved.

MOSAIC: a chemical-genetic interaction data repository and web resource for exploring chemical modes of action.

PubMed

Nelson, Justin; Simpkins, Scott W; Safizadeh, Hamid; Li, Sheena C; Piotrowski, Jeff S; Hirano, Hiroyuki; Yashiroda, Yoko; Osada, Hiroyuki; Yoshida, Minoru; Boone, Charles; Myers, Chad L

2018-04-01

Chemical-genomic approaches that map interactions between small molecules and genetic perturbations offer a promising strategy for functional annotation of uncharacterized bioactive compounds. We recently developed a new high-throughput platform for mapping chemical-genetic (CG) interactions in yeast that can be scaled to screen large compound collections, and we applied this system to generate CG interaction profiles for more than 13 000 compounds. When integrated with the existing global yeast genetic interaction network, CG interaction profiles can enable mode-of-action prediction for previously uncharacterized compounds as well as discover unexpected secondary effects for known drugs. To facilitate future analysis of these valuable data, we developed a public database and web interface named MOSAIC. The website provides a convenient interface for querying compounds, bioprocesses (Gene Ontology terms) and genes for CG information including direct CG interactions, bioprocesses and gene-level target predictions. MOSAIC also provides access to chemical structure information of screened molecules, chemical-genomic profiles and the ability to search for compounds sharing structural and functional similarity. This resource will be of interest to chemical biologists for discovering new small molecule probes with specific modes-of-action as well as computational biologists interested in analysing CG interaction networks. MOSAIC is available at http://mosaic.cs.umn.edu. hisyo@riken.jp, yoshidam@riken.jp, charlie.boone@utoronto.ca or chadm@umn.edu. Supplementary data are available at Bioinformatics online.

Genomics-assisted breeding for boosting crop improvement in pigeonpea (Cajanus cajan)

PubMed Central

Pazhamala, Lekha; Saxena, Rachit K.; Singh, Vikas K.; Sameerkumar, C. V.; Kumar, Vinay; Sinha, Pallavi; Patel, Kishan; Obala, Jimmy; Kaoneka, Seleman R.; Tongoona, P.; Shimelis, Hussein A.; Gangarao, N. V. P. R.; Odeny, Damaris; Rathore, Abhishek; Dharmaraj, P. S.; Yamini, K. N.; Varshney, Rajeev K.

2015-01-01

Pigeonpea is an important pulse crop grown predominantly in the tropical and sub-tropical regions of the world. Although pigeonpea growing area has considerably increased, yield has remained stagnant for the last six decades mainly due to the exposure of the crop to various biotic and abiotic constraints. In addition, low level of genetic variability and limited genomic resources have been serious impediments to pigeonpea crop improvement through modern breeding approaches. In recent years, however, due to the availability of next generation sequencing and high-throughput genotyping technologies, the scenario has changed tremendously. The reduced sequencing costs resulting in the decoding of the pigeonpea genome has led to the development of various genomic resources including molecular markers, transcript sequences and comprehensive genetic maps. Mapping of some important traits including resistance to Fusarium wilt and sterility mosaic disease, fertility restoration, determinacy with other agronomically important traits have paved the way for applying genomics-assisted breeding (GAB) through marker assisted selection as well as genomic selection (GS). This would accelerate the development and improvement of both varieties and hybrids in pigeonpea. Particularly for hybrid breeding programme, mitochondrial genomes of cytoplasmic male sterile (CMS) lines, maintainers and hybrids have been sequenced to identify genes responsible for cytoplasmic male sterility. Furthermore, several diagnostic molecular markers have been developed to assess the purity of commercial hybrids. In summary, pigeonpea has become a genomic resources-rich crop and efforts have already been initiated to integrate these resources in pigeonpea breeding. PMID:25741349

Options and legal requirements for national and regional animal genetic resources collections

USDA-ARS?s Scientific Manuscript database

The contraction of animal genetic resources on a global scale has motivated countries to establish gene banks as a mechanism to conserve national resources. Gene banks should establish a set of policies that insure they are complying with national laws. The two primary areas of consideration are ho...

Development and characterization of a new TILLING population of common bread wheat (Triticum aestivum L.).

PubMed

Chen, Liang; Huang, Linzhou; Min, Donghong; Phillips, Andy; Wang, Shiqiang; Madgwick, Pippa J; Parry, Martin A J; Hu, Yin-Gang

2012-01-01

Mutagenesis is an important tool in crop improvement. However, the hexaploid genome of wheat (Triticum aestivum L.) presents problems in identifying desirable genetic changes based on phenotypic screening due to gene redundancy. TILLING (Targeting Induced Local Lesions IN Genomes), a powerful reverse genetic strategy that allows the detection of induced point mutations in individuals of the mutagenized populations, can address the major challenge of linking sequence information to the biological function of genes and can also identify novel variation for crop breeding. Wheat is especially well-suited for TILLING due to the high mutation densities tolerated by polyploids. However, only a few wheat TILLING populations are currently available in the world, which is far from satisfying the requirement of researchers and breeders in different growing environments. In addition, current TILLING screening protocols require costly fluorescence detection systems, limiting their use, especially in developing countries. We developed a new TILLING resource comprising 2610 M(2) mutants in a common wheat cultivar 'Jinmai 47'. Numerous phenotypes with altered morphological and agronomic traits were observed from the M(2) and M(3) lines in the field. To simplify the procedure and decrease costs, we use unlabeled primers and either non-denaturing polyacrylamide gels or agarose gels for mutation detection. The value of this new resource was tested using PCR with RAPD and Intron-spliced junction (ISJ) primers, and also TILLING in three selected candidate genes, in 300 and 512 mutant lines, revealing high mutation densities of 1/34 kb by RAPD/ISJ analysis and 1/47 kb by TILLING. In total, 31 novel alleles were identified in the 3 targeted genes and confirmed by sequencing. The results indicate that this mutant population represents a useful resource for the wheat research community. We hope that the use of this reverse genetics resource will provide novel allelic diversity for wheat improvement and functional genomics.

Ancient orphan crop joins modern era: gene-based SNP discovery and mapping in lentil.

PubMed

Sharpe, Andrew G; Ramsay, Larissa; Sanderson, Lacey-Anne; Fedoruk, Michael J; Clarke, Wayne E; Li, Rong; Kagale, Sateesh; Vijayan, Perumal; Vandenberg, Albert; Bett, Kirstin E

2013-03-18

The genus Lens comprises a range of closely related species within the galegoid clade of the Papilionoideae family. The clade includes other important crops (e.g. chickpea and pea) as well as a sequenced model legume (Medicago truncatula). Lentil is a global food crop increasing in importance in the Indian sub-continent and elsewhere due to its nutritional value and quick cooking time. Despite this importance there has been a dearth of genetic and genomic resources for the crop and this has limited the application of marker-assisted selection strategies in breeding. We describe here the development of a deep and diverse transcriptome resource for lentil using next generation sequencing technology. The generation of data in multiple cultivated (L. culinaris) and wild (L. ervoides) genotypes together with the utilization of a bioinformatics workflow enabled the identification of a large collection of SNPs and the subsequent development of a genotyping platform that was used to establish the first comprehensive genetic map of the L. culinaris genome. Extensive collinearity with M. truncatula was evident on the basis of sequence homology between mapped markers and the model genome and large translocations and inversions relative to M. truncatula were identified. An estimate for the time divergence of L. culinaris from L. ervoides and of both from M. truncatula was also calculated. The availability of the genomic and derived molecular marker resources presented here will help change lentil breeding strategies and lead to increased genetic gain in the future.

Learning about Charcot-Marie-Tooth Disease

MedlinePlus

... Links for Patient Care Education All About the Human Genome Project Fact Sheets Genetic Education Resources for Teachers ... Education Kit Online Genetics Education Resources Smithsonian NHGRI Genome ... Subjects Research Informed Consent for Genomics Research Intellectual ...

Transcriptomic resources for the medicinal legume Mucuna pruriens: de novo transcriptome assembly, annotation, identification and validation of EST-SSR markers.

PubMed

Sathyanarayana, N; Pittala, Ranjith Kumar; Tripathi, Pankaj Kumar; Chopra, Ratan; Singh, Heikham Russiachand; Belamkar, Vikas; Bhardwaj, Pardeep Kumar; Doyle, Jeff J; Egan, Ashley N

2017-05-25

The medicinal legume Mucuna pruriens (L.) DC. has attracted attention worldwide as a source of the anti-Parkinson's drug L-Dopa. It is also a popular green manure cover crop that offers many agronomic benefits including high protein content, nitrogen fixation and soil nutrients. The plant currently lacks genomic resources and there is limited knowledge on gene expression, metabolic pathways, and genetics of secondary metabolite production. Here, we present transcriptomic resources for M. pruriens, including a de novo transcriptome assembly and annotation, as well as differential transcript expression analyses between root, leaf, and pod tissues. We also develop microsatellite markers and analyze genetic diversity and population structure within a set of Indian germplasm accessions. One-hundred ninety-one million two hundred thirty-three thousand two hundred forty-two bp cleaned reads were assembled into 67,561 transcripts with mean length of 626 bp and N50 of 987 bp. Assembled sequences were annotated using BLASTX against public databases with over 80% of transcripts annotated. We identified 7,493 simple sequence repeat (SSR) motifs, including 787 polymorphic repeats between the parents of a mapping population. 134 SSRs from expressed sequenced tags (ESTs) were screened against 23 M. pruriens accessions from India, with 52 EST-SSRs retained after quality control. Population structure analysis using a Bayesian framework implemented in fastSTRUCTURE showed nearly similar groupings as with distance-based (neighbor-joining) and principal component analyses, with most of the accessions clustering per geographical origins. Pair-wise comparison of transcript expression in leaves, roots and pods identified 4,387 differentially expressed transcripts with the highest number occurring between roots and leaves. Differentially expressed transcripts were enriched with transcription factors and transcripts annotated as belonging to secondary metabolite pathways. The M. pruriens transcriptomic resources generated in this study provide foundational resources for gene discovery and development of molecular markers. Polymorphic SSRs identified can be used for genetic diversity, marker-trait analyses, and development of functional markers for crop improvement. The results of differential expression studies can be used to investigate genes involved in L-Dopa synthesis and other key metabolic pathways in M. pruriens.

Development and Evolution of Character Displacement

PubMed Central

Pfennig, David W.; Pfennig, Karin S.

2012-01-01

Character displacement occurs when competition for either resources or successful reproduction imposes divergent selection on interacting species, causing divergence in traits associated with resource use or reproduction. Here, we describe how character displacement can be mediated either by genetically canalized changes (i.e., changes that reflect allelic or genotype frequency changes) or by phenotypic plasticity. We also discuss how these two mechanisms influence the tempo of character displacement. Specifically, we suggest that, under some conditions, character displacement mediated by phenotypic plasticity might occur more rapidly than that mediated by genetically canalized changes. Finally, we describe how these two mechanisms may act together and determine character displacement’s mode, such that it proceeds through an initial phase in which trait divergence is environmentally induced to a later phase in which divergence becomes genetically canalized. This plasticity-first hypothesis predicts that character displacement should be generally mediated by ancestral plasticity and that it will arise similarly in multiple, independently evolving populations. We conclude by highlighting future directions for research that would test these predictions. PMID:22257002

Establishing a Twin Register: An Invaluable Resource for (Behavior) Genetic, Epidemiological, Biomarker, and 'Omics' Studies.

PubMed

Odintsova, Veronika V; Willemsen, Gonneke; Dolan, Conor V; Hottenga, Jouke-Jan; Martin, Nicholas G; Slagboom, P Eline; Ordoñana, Juan R; Boomsma, Dorret I

2018-06-01

Twin registers are wonderful research resources for research applications in medical and behavioral genetics, epidemiology, psychology, molecular genetics, and other areas of research. New registers continue to be launched all over the world as researchers from different disciplines recognize the potential to boost and widen their research agenda. In this article, we discuss multiple aspects that need to be taken into account when initiating a register, from its preliminary sketch to its actual development. This encompasses aspects related to the strategic planning and key elements of research designs, promotion and management of a twin register, including recruitment and retaining of twins and family members of twins, phenotyping, database organization, and collaborations between registers. We also present information on questions unique to twin registers and twin-biobanks, such as the assessment of zygosity by SNP arrays, the design of (biomarker) studies involving related participants, and the analyses of clustered data. Altogether, we provide a number of basic guidelines and recommendations for reflection when planning a twin register.

Genetic diversity of populations and clones of Rhopilema esculentum in China based on AFLP analysis

NASA Astrophysics Data System (ADS)

Qiao, Hongjin; Liu, Xiangquan; Zhang, Xijia; Jiang, Haibin; Wang, Jiying; Zhang, Limin

2013-03-01

Amplified fragment length polymorphisms (AFLP) markers were developed to assess the genetic variation of populations and clones of Rhopilema esculentum Kishinouye (Scyphozoa, Rhizostomatidae). One hundred and seventy-nine loci from 56 individuals of two hatchery populations and two wild populations were genotyped with five primer combinations. The polymorphic ratio, Shannon's diversity index and average heterozygosity were 70.3%, 0.346 and 0.228 for the white hatchery population, 74.3%, 0.313, and 0.201 for the red hatchery population, 79.3%, 0.349, and 0.224 for the Jiangsu wild population, and 74.9%, 0.328 and 0.210 for the Penglai wild population, respectively. Thus, all populations had a relatively high level of genetic diversity. A specific band was identified that could separate the white from the red hatchery population. There was 84.85% genetic differentiation within populations. Individual cluster analysis using unweighted pair-group method with arithmetic mean (UPGMA) suggested that hatchery populations and wild populations could be divided. For the hatchery populations, the white and red populations clustered separately; however, for the wild populations, Penglai and Jiangsu populations clustered together. The genetic diversity at the clone level was also determined. Our data suggest that there are relatively high genetic diversities within populations but low genetic differentiation between populations, which may be related to the long-term use of germplasm resources from Jiangsu Province for artificial seeding and releasing. These findings will benefit the artificial seeding and conservation of the germplasm resources.

Genetics Home Reference: Pompe disease

MedlinePlus

... Genetic Testing (2 links) Genetic Testing Registry: Glycogen storage disease type II, infantile Genetic Testing Registry: Glycogen storage disease, type II Other Diagnosis and Management Resources ( ...

The Life Course Health Development Model: A Guide to Children's Health Care Policy and Practice

ERIC Educational Resources Information Center

Halfon, Neal; Russ, Shirley; Regalado, Michael

2005-01-01

As medical knowledge and treatments improve, pediatricians' role in promoting children's health continues to change. Genetics and early experiences may have long-term effects on health and development. Theoretical models that influence providers' decisions about the use of health-care resources are: the disease model, the neuromaturational model,…

Legal issues in plant germplasm collecting

USDA-ARS?s Scientific Manuscript database

Many developments have occurred in the legal environment governing plant germplasm collecting since the first edition of this Manual. These include the adoption of the Global Plan of Action for the Conservation and Sustainable Utilization of Plant Genetic Resources for Food and Agriculture (the Glob...

Widespread applications of citrus cryopreservation

USDA-ARS?s Scientific Manuscript database

Citrus genetic resources can now be successfully cryopreserved, which means that they can be placed into long-term storage at liquid nitrogen temperatures. This cryopreservation technology was specifically developed to address the immediate need to have secure long-term back-up storage for citrus co...

Genomics of Tropical Fruit Tree Crops

USDA-ARS?s Scientific Manuscript database

The genetic improvement of tropical fruit trees is limited when compared to progress achieved in temperate fruit trees and annual crops. Tropical fruit tree breeding programs require significant resources to develop new cultivars that are adapted to modern shipping and storage requirements. The use...

Adaptive responses and disruptive effects: how major wildfire influences kinship-based social interactions in a forest marsupial.

PubMed

Banks, Sam C; Blyton, Michaela D J; Blair, David; McBurney, Lachlan; Lindenmayer, David B

2012-02-01

Environmental disturbance is predicted to play a key role in the evolution of animal social behaviour. This is because disturbance affects key factors underlying social systems, such as demography, resource availability and genetic structure. However, because natural disturbances are unpredictable there is little information on their effects on social behaviour in wild populations. Here, we investigated how a major wildfire affected cooperation (sharing of hollow trees) by a hollow-dependent marsupial. We based two alternative social predictions on the impacts of fire on population density, genetic structure and resources. We predicted an adaptive social response from previous work showing that kin selection in den-sharing develops as competition for den resources increases. Thus, kin selection should occur in burnt areas because the fire caused loss of the majority of hollow-bearing trees, but no detectable mortality. Alternatively, fire may have a disruptive social effect, whereby postfire home range-shifts 'neutralize' fine-scale genetic structure, thereby removing opportunities for kin selection between neighbours. Both predictions occurred: the disruptive social effect in burnt habitat and the adaptive social response in adjacent unburnt habitat. The latter followed a massive demographic influx to unburnt 'refuge' habitat that increased competition for dens, leading to a density-related kin selection response. Our results show remarkable short-term plasticity of animal social behaviour and demonstrate how the social effects of disturbance extend into undisturbed habitat owing to landscape-scale demographic shifts. We predicted long-term changes in kinship-based cooperative behaviour resulting from the genetic and resource impacts of forecast changes to fire regimes in these forests. © 2011 Blackwell Publishing Ltd.

Accelerating Precision Drug Development and Drug Repurposing by Leveraging Human Genetics

PubMed Central

Shirey-Rice, Jana K.; Lavieri, Robert R.; Jerome, Rebecca N.; Zaleski, Nicole M.; Aronoff, David M.; Bastarache, Lisa; Niu, Xinnan; Holroyd, Kenneth J.; Roden, Dan M.; Skaar, Eric P.; Niswender, Colleen M.; Marnett, Lawrence J.; Lindsley, Craig W.; Ekstrom, Leeland B.; Bentley, Alan R.; Bernard, Gordon R.; Hong, Charles C.; Denny, Joshua C.

2017-01-01

Abstract The potential impact of using human genetic data linked to longitudinal electronic medical records on drug development is extraordinary; however, the practical application of these data necessitates some organizational innovations. Vanderbilt has created resources such as an easily queried database of >2.6 million de-identified electronic health records linked to BioVU, which is a DNA biobank with more than 230,000 unique samples. To ensure these data are used to maximally benefit and accelerate both de novo drug discovery and drug repurposing efforts, we created the Accelerating Drug Development and Repurposing Incubator, a multidisciplinary think tank of experts in various therapeutic areas within both basic and clinical science as well as experts in legal, business, and other operational domains. The Incubator supports a diverse pipeline of drug indication finding projects, leveraging the natural experiment of human genetics. PMID:28379727

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tumuluru, Jaya Shankar; McCulloch, Richard Chet James

In this work a new hybrid genetic algorithm was developed which combines a rudimentary adaptive steepest ascent hill climbing algorithm with a sophisticated evolutionary algorithm in order to optimize complex multivariate design problems. By combining a highly stochastic algorithm (evolutionary) with a simple deterministic optimization algorithm (adaptive steepest ascent) computational resources are conserved and the solution converges rapidly when compared to either algorithm alone. In genetic algorithms natural selection is mimicked by random events such as breeding and mutation. In the adaptive steepest ascent algorithm each variable is perturbed by a small amount and the variable that caused the mostmore » improvement is incremented by a small step. If the direction of most benefit is exactly opposite of the previous direction with the most benefit then the step size is reduced by a factor of 2, thus the step size adapts to the terrain. A graphical user interface was created in MATLAB to provide an interface between the hybrid genetic algorithm and the user. Additional features such as bounding the solution space and weighting the objective functions individually are also built into the interface. The algorithm developed was tested to optimize the functions developed for a wood pelleting process. Using process variables (such as feedstock moisture content, die speed, and preheating temperature) pellet properties were appropriately optimized. Specifically, variables were found which maximized unit density, bulk density, tapped density, and durability while minimizing pellet moisture content and specific energy consumption. The time and computational resources required for the optimization were dramatically decreased using the hybrid genetic algorithm when compared to MATLAB's native evolutionary optimization tool.« less

An Integrated Korean Biodiversity and Genetic Information Retrieval System

PubMed Central

Lim, Jeongheui; Bhak, Jong; Oh, Hee-Mock; Kim, Chang-Bae; Park, Yong-Ha; Paek, Woon Kee

2008-01-01

Background On-line biodiversity information databases are growing quickly and being integrated into general bioinformatics systems due to the advances of fast gene sequencing technologies and the Internet. These can reduce the cost and effort of performing biodiversity surveys and genetic searches, which allows scientists to spend more time researching and less time collecting and maintaining data. This will cause an increased rate of knowledge build-up and improve conservations. The biodiversity databases in Korea have been scattered among several institutes and local natural history museums with incompatible data types. Therefore, a comprehensive database and a nation wide web portal for biodiversity information is necessary in order to integrate diverse information resources, including molecular and genomic databases. Results The Korean Natural History Research Information System (NARIS) was built and serviced as the central biodiversity information system to collect and integrate the biodiversity data of various institutes and natural history museums in Korea. This database aims to be an integrated resource that contains additional biological information, such as genome sequences and molecular level diversity. Currently, twelve institutes and museums in Korea are integrated by the DiGIR (Distributed Generic Information Retrieval) protocol, with Darwin Core2.0 format as its metadata standard for data exchange. Data quality control and statistical analysis functions have been implemented. In particular, integrating molecular and genetic information from the National Center for Biotechnology Information (NCBI) databases with NARIS was recently accomplished. NARIS can also be extended to accommodate other institutes abroad, and the whole system can be exported to establish local biodiversity management servers. Conclusion A Korean data portal, NARIS, has been developed to efficiently manage and utilize biodiversity data, which includes genetic resources. NARIS aims to be integral in maximizing bio-resource utilization for conservation, management, research, education, industrial applications, and integration with other bioinformation data resources. It can be found at . PMID:19091024

Transporter engineering in biomass utilization by yeast.

PubMed

Hara, Kiyotaka Y; Kobayashi, Jyumpei; Yamada, Ryosuke; Sasaki, Daisuke; Kuriya, Yuki; Hirono-Hara, Yoko; Ishii, Jun; Araki, Michihiro; Kondo, Akihiko

2017-11-01

Biomass resources are attractive carbon sources for bioproduction because of their sustainability. Many studies have been performed using biomass resources to produce sugars as carbon sources for cell factories. Expression of biomass hydrolyzing enzymes in cell factories is an important approach for constructing biomass-utilizing bioprocesses because external addition of these enzymes is expensive. In particular, yeasts have been extensively engineered to be cell factories that directly utilize biomass because of their manageable responses to many genetic engineering tools, such as gene expression, deletion and editing. Biomass utilizing bioprocesses have also been developed using these genetic engineering tools to construct metabolic pathways. However, sugar input and product output from these cells are critical factors for improving bioproduction along with biomass utilization and metabolic pathways. Transporters are key components for efficient input and output activities. In this review, we focus on transporter engineering in yeast to enhance bioproduction from biomass resources. © FEMS 2017. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Genetics Home Reference: Paget disease of bone

MedlinePlus

... genetic cause of classic Paget disease of bone , accounting for 10 to 50 percent of cases that ... be inherited? More about Inheriting Genetic Conditions Diagnosis & Management Resources Genetic Testing (6 links) Genetic Testing Registry: ...

Molecular genetics and genomics of the Rosoideae: state of the art and future perspectives

PubMed Central

Longhi, Sara; Giongo, Lara; Buti, Matteo; Surbanovski, Nada; Viola, Roberto; Velasco, Riccardo; Ward, Judson A; Sargent, Daniel J

2014-01-01

The Rosoideae is a subfamily of the Rosaceae that contains a number of species of economic importance, including the soft fruit species strawberry (Fragaria ×ananassa), red (Rubus idaeus) and black (Rubus occidentalis) raspberries, blackberries (Rubus spp.) and one of the most economically important cut flower genera, the roses (Rosa spp.). Molecular genetics and genomics resources for the Rosoideae have developed rapidly over the past two decades, beginning with the development and application of a number of molecular marker types including restriction fragment length polymorphisms, amplified fragment length polymorphisms and microsatellites, and culminating in the recent publication of the genome sequence of the woodland strawberry, Fragaria vesca, and the development of high throughput single nucleotide polymorphism (SNP)-genotyping resources for Fragaria, Rosa and Rubus. These tools have been used to identify genes and other functional elements that control traits of economic importance, to study the evolution of plant genome structure within the subfamily, and are beginning to facilitate genomic-assisted breeding through the development and deployment of markers linked to traits such as aspects of fruit quality, disease resistance and the timing of flowering. In this review, we report on the developments that have been made over the last 20 years in the field of molecular genetics and structural genomics within the Rosoideae, comment on how the knowledge gained will improve the efficiency of cultivar development and discuss how these advances will enhance our understanding of the biological processes determining agronomically important traits in all Rosoideae species. PMID:26504527

gQTL: A Web Application for QTL Analysis Using the Collaborative Cross Mouse Genetic Reference Population.

PubMed

Konganti, Kranti; Ehrlich, Andre; Rusyn, Ivan; Threadgill, David W

2018-06-07

Multi-parental recombinant inbred populations, such as the Collaborative Cross (CC) mouse genetic reference population, are increasingly being used for analysis of quantitative trait loci (QTL). However specialized analytic software for these complex populations is typically built in R that works only on command-line, which limits the utility of these powerful resources for many users. To overcome analytic limitations, we developed gQTL, a web accessible, simple graphical user interface application based on the DOQTL platform in R to perform QTL mapping using data from CC mice. Copyright © 2018, G3: Genes, Genomes, Genetics.

PineElm_SSRdb: a microsatellite marker database identified from genomic, chloroplast, mitochondrial and EST sequences of pineapple (Ananas comosus (L.) Merrill).

PubMed

Chaudhary, Sakshi; Mishra, Bharat Kumar; Vivek, Thiruvettai; Magadum, Santoshkumar; Yasin, Jeshima Khan

2016-01-01

Simple Sequence Repeats or microsatellites are resourceful molecular genetic markers. There are only few reports of SSR identification and development in pineapple. Complete genome sequence of pineapple available in the public domain can be used to develop numerous novel SSRs. Therefore, an attempt was made to identify SSRs from genomic, chloroplast, mitochondrial and EST sequences of pineapple which will help in deciphering genetic makeup of its germplasm resources. A total of 359511 SSRs were identified in pineapple (356385 from genome sequence, 45 from chloroplast sequence, 249 in mitochondrial sequence and 2832 from EST sequences). The list of EST-SSR markers and their details are available in the database. PineElm_SSRdb is an open source database available for non-commercial academic purpose at http://app.bioelm.com/ with a mapping tool which can develop circular maps of selected marker set. This database will be of immense use to breeders, researchers and graduates working on Ananas spp. and to others working on cross-species transferability of markers, investigating diversity, mapping and DNA fingerprinting.

An integrated map of genetic variation from 1,092 human genomes

PubMed Central

2012-01-01

Summary Through characterising the geographic and functional spectrum of human genetic variation, the 1000 Genomes Project aims to build a resource to help understand the genetic contribution to disease. We describe the genomes of 1,092 individuals from 14 populations, constructed using a combination of low-coverage whole-genome and exome sequencing. By developing methodologies to integrate information across multiple algorithms and diverse data sources we provide a validated haplotype map of 38 million SNPs, 1.4 million indels and over 14 thousand larger deletions. We show that individuals from different populations carry different profiles of rare and common variants and that low-frequency variants show substantial geographic differentiation, which is further increased by the action of purifying selection. We show that evolutionary conservation and coding consequence are key determinants of the strength of purifying selection, that rare-variant load varies substantially across biological pathways and that each individual harbours hundreds of rare non-coding variants at conserved sites, such as transcription-factor-motif disrupting changes. This resource, which captures up to 98% of accessible SNPs at a frequency of 1% in populations of medical genetics focus, enables analysis of common and low-frequency variants in individuals from diverse, including admixed, populations. PMID:23128226

Utilization of farm animal genetic resources in a changing agro-ecological environment in the Nordic countries.

PubMed

Kantanen, Juha; Løvendahl, Peter; Strandberg, Erling; Eythorsdottir, Emma; Li, Meng-Hua; Kettunen-Præbel, Anne; Berg, Peer; Meuwissen, Theo

2015-01-01

Livestock production is the most important component of northern European agriculture and contributes to and will be affected by climate change. Nevertheless, the role of farm animal genetic resources in the adaptation to new agro-ecological conditions and mitigation of animal production's effects on climate change has been inadequately discussed despite there being several important associations between animal genetic resources and climate change issues. The sustainability of animal production systems and future food security require access to a wide diversity of animal genetic resources. There are several genetic questions that should be considered in strategies promoting adaptation to climate change and mitigation of environmental effects of livestock production. For example, it may become important to choose among breeds and even among farm animal species according to their suitability to a future with altered production systems. Some animals with useful phenotypes and genotypes may be more useful than others in the changing environment. Robust animal breeds with the potential to adapt to new agro-ecological conditions and tolerate new diseases will be needed. The key issue in mitigation of harmful greenhouse gas effects induced by livestock production is the reduction of methane (CH4) emissions from ruminants. There are differences in CH4 emissions among breeds and among individual animals within breeds that suggest a potential for improvement in the trait through genetic selection. Characterization of breeds and individuals with modern genomic tools should be applied to identify breeds that have genetically adapted to marginal conditions and to get critical information for breeding and conservation programs for farm animal genetic resources. We conclude that phenotyping and genomic technologies and adoption of new breeding approaches, such as genomic selection introgression, will promote breeding for useful characters in livestock species.

Utilization of farm animal genetic resources in a changing agro-ecological environment in the Nordic countries

PubMed Central

Kantanen, Juha; Løvendahl, Peter; Strandberg, Erling; Eythorsdottir, Emma; Li, Meng-Hua; Kettunen-Præbel, Anne; Berg, Peer; Meuwissen, Theo

2015-01-01

Livestock production is the most important component of northern European agriculture and contributes to and will be affected by climate change. Nevertheless, the role of farm animal genetic resources in the adaptation to new agro-ecological conditions and mitigation of animal production’s effects on climate change has been inadequately discussed despite there being several important associations between animal genetic resources and climate change issues. The sustainability of animal production systems and future food security require access to a wide diversity of animal genetic resources. There are several genetic questions that should be considered in strategies promoting adaptation to climate change and mitigation of environmental effects of livestock production. For example, it may become important to choose among breeds and even among farm animal species according to their suitability to a future with altered production systems. Some animals with useful phenotypes and genotypes may be more useful than others in the changing environment. Robust animal breeds with the potential to adapt to new agro-ecological conditions and tolerate new diseases will be needed. The key issue in mitigation of harmful greenhouse gas effects induced by livestock production is the reduction of methane (CH4) emissions from ruminants. There are differences in CH4 emissions among breeds and among individual animals within breeds that suggest a potential for improvement in the trait through genetic selection. Characterization of breeds and individuals with modern genomic tools should be applied to identify breeds that have genetically adapted to marginal conditions and to get critical information for breeding and conservation programs for farm animal genetic resources. We conclude that phenotyping and genomic technologies and adoption of new breeding approaches, such as genomic selection introgression, will promote breeding for useful characters in livestock species. PMID:25767477

Cryopreservation of apple (Malus spp.): development, progress and future prospects

USDA-ARS?s Scientific Manuscript database

Apple (Malus sp.) is one of the most economically important temperate fruit crops. Wild Malus genetic resources and existing cultivars provide valuable genes for breeding new elite cultivars and rootstocks through traditional and biotechnological breeding programs. Over the last three decades, great...

Determining mutation density using Restriction Enzyme Sequence Comparative Analysis (RESCAN)

USDA-ARS?s Scientific Manuscript database

The average mutation density of a mutant population is a major consideration when developing resources for the efficient, cost-effective implementation of reverse genetics methods such as Targeting of Induced Local Lesions in Genomes (TILLING). Reliable estimates of mutation density can be achieved ...

Applications of metagenomics for industrial bioproducts

USDA-ARS?s Scientific Manuscript database

Recent progress in mining the rich genetic resource of non-culturable microbes has led to the discovery of new genes, enzymes, and natural products. The impact of metagenomics is witnessed in the development of commodity and fine chemicals, agrochemicals and pharmaceuticals where the benefit of enz...

Cryoconservation of animal genetic resources. Animal Production and Health Guidelines No. 12

USDA-ARS?s Scientific Manuscript database

Livestock agriculture is in a period of tumultuous change and upheaval. General economic development, and population growth and mobility, have increased demand for livestock products, but have also placed pressures on the sustainability of rural environments and animal production systems. Livestock ...

Date Palm Genetic Diversity Analysis Using Microsatellite Polymorphism.

PubMed

Khierallah, Hussam S M; Bader, Saleh M; Hamwieh, Alladin; Baum, Michael

2017-01-01

Date palm (Phoenix dactylifera L.) is considered one of the great socioeconomic resources in the Middle East and the Arab regions. The tree has been and still is at the center of the comprehensive agricultural development. The number of known date palm cultivars, distributed worldwide, is approximately 3000. The success of genetic diversity conservation or any breeding program depends on an understanding of the amount and distribution of the genetic variation already in existence in the genetic pool. Development of suitable DNA molecular markers for this tree may allow researchers to estimate genetic diversity, which will ultimately lead to the genetic conservation of date palm. Simple sequence repeats (SSRs) are DNA strands, consisting of tandemly repeated mono-, di-, tri-, tetra-, or penta-nucleotide units that are arranged throughout the genomes of most eukaryotic species. Microsatellite markers, developed from genomic libraries, belong to either the transcribed region or the non-transcribed region of the genome, and there is rarely available information on their functions. Microsatellite sequences are especially suited to distinguish closely related genotypes due to a high degree of variability making them ideally suitable in population studies and the identification of closely related cultivars. This chapter focuses on the methods employed to characterize date palm genotypes using SSR markers.

Development of Genomic Simple Sequence Repeats (SSR) by Enrichment Libraries in Date Palm.

PubMed

Al-Faifi, Sulieman A; Migdadi, Hussein M; Algamdi, Salem S; Khan, Mohammad Altaf; Al-Obeed, Rashid S; Ammar, Megahed H; Jakse, Jerenj

2017-01-01

Development of highly informative markers such as simple sequence repeats (SSR) for cultivar identification and germplasm characterization and management is essential for date palms genetic studies. The present study documents the development of SSR markers and assesses genetic relationships of commonly grown date palm (Phoenix dactylifera L.) cultivars in different geographical regions of Saudi Arabia. A total of 93 novel simple sequence repeat (SSR) markers were screened for their ability to detect polymorphism in date palm. Around 71% of genomic SSRs are dinucleotide, 25% trinucleotide, 3% tetranucleotide, and 1% pentanucleotide motives and show 100% polymorphism. The Unweighted Pair Group Method with Arithmetic Mean (UPGMA) cluster analysis illustrates that cultivars trend to group according to their class of maturity, region of cultivation, and fruit color. Analysis of molecular variations (AMOVA) reveals genetic variation among and within cultivars of 27% and 73%, respectively, according to the geographical distribution of the cultivars. Developed microsatellite markers are of additional value to date palm characterization, tools which can be used by researchers in population genetics, cultivar identification, as well as genetic resource exploration and management. The cultivars tested exhibited a significant amount of genetic diversity and could be suitable for successful breeding programs. Genomic sequences generated from this study are available at the National Center for Biotechnology Information (NCBI), Sequence Read Archive (Accession numbers. LIBGSS_039019).

The genetic difference principle.

PubMed

Farrelly, Colin

2004-01-01

In the newly emerging debates about genetics and justice three distinct principles have begun to emerge concerning what the distributive aim of genetic interventions should be. These principles are: genetic equality, a genetic decent minimum, and the genetic difference principle. In this paper, I examine the rationale of each of these principles and argue that genetic equality and a genetic decent minimum are ill-equipped to tackle what I call the currency problem and the problem of weight. The genetic difference principle is the most promising of the three principles and I develop this principle so that it takes seriously the concerns of just health care and distributive justice in general. Given the strains on public funds for other important social programmes, the costs of pursuing genetic interventions and the nature of genetic interventions, I conclude that a more lax interpretation of the genetic difference principle is appropriate. This interpretation stipulates that genetic inequalities should be arranged so that they are to the greatest reasonable benefit of the least advantaged. Such a proposal is consistent with prioritarianism and provides some practical guidance for non-ideal societies--that is, societies that do not have the endless amount of resources needed to satisfy every requirement of justice.

Recommendations for genetic variation data capture in developing countries to ensure a comprehensive worldwide data collection.

PubMed

Patrinos, George P; Al Aama, Jumana; Al Aqeel, Aida; Al-Mulla, Fahd; Borg, Joseph; Devereux, Andrew; Felice, Alex E; Macrae, Finlay; Marafie, Makia J; Petersen, Michael B; Qi, Ming; Ramesar, Rajkumar S; Zlotogora, Joel; Cotton, Richard G H

2011-01-01

Developing countries have significantly contributed to the elucidation of the genetic basis of both common and rare disorders, providing an invaluable resource of cases due to large family sizes, consanguinity, and potential founder effects. Moreover, the recognized depth of genomic variation in indigenous African populations, reflecting the ancient origins of humanity on the African continent, and the effect of selection pressures on the genome, will be valuable in understanding the range of both pathological and nonpathological variations. The involvement of these populations in accurately documenting the extant genetic heterogeneity is more than essential. Developing nations are regarded as key contributors to the Human Variome Project (HVP; http://www.humanvariomeproject.org), a major effort to systematically collect mutations that contribute to or cause human disease and create a cyber infrastructure to tie databases together. However, biomedical research has not been the primary focus in these countries even though such activities are likely to produce economic and health benefits for all. Here, we propose several recommendations and guidelines to facilitate participation of developing countries in genetic variation data documentation, ensuring an accurate and comprehensive worldwide data collection. We also summarize a few well-coordinated genetic data collection initiatives that would serve as paradigms for similar projects.

Prototype of a Standards-Based EHR and Genetic Test Reporting Tool Coupled with HL7-Compliant Infobuttons

PubMed Central

Crump, Jacob K.; Del Fiol, Guilherme; Williams, Marc S.; Freimuth, Robert R.

2018-01-01

Integration of genetic information is becoming increasingly important in clinical practice. However, genetic information is often ambiguous and difficult to understand, and clinicians have reported low-self-efficacy in integrating genetics into their care routine. The Health Level Seven (HL7) Infobutton standard helps to integrate online knowledge resources within Electronic Health Records (EHRs) and is required for EHR certification in the US. We implemented a prototype of a standards-based genetic reporting application coupled with infobuttons leveraging the Infobutton and Fast Healthcare Interoperability Resources (FHIR) Standards. Infobutton capabilities were provided by Open Infobutton, an open source package compliant with the HL7 Infobutton Standard. The resulting prototype demonstrates how standards-based reporting of genetic results, coupled with curated knowledge resources, can provide dynamic access to clinical knowledge on demand at the point of care. The proposed functionality can be enabled within any EHR system that has been certified through the US Meaningful Use program.

Resources for Systems Genetics.

PubMed

Williams, Robert W; Williams, Evan G

2017-01-01

A key characteristic of systems genetics is its reliance on populations that vary to a greater or lesser degree in genetic complexity-from highly admixed populations such as the Collaborative Cross and Diversity Outcross to relatively simple crosses such as sets of consomic strains and reduced complexity crosses. This protocol is intended to help investigators make more informed decisions about choices of resources given different types of questions. We consider factors such as costs, availability, and ease of breeding for common scenarios. In general, we recommend using complementary resources and minimizing depth of resampling of any given genome or strain.

Development of a global conservation strategy for citrus genetic resources

USDA-ARS?s Scientific Manuscript database

Citrus is an economically important world tree fruit crop with production in more than 146 countries. The center of origin for citrus is considered to be Southeastern Asia including southern China, northeastern India, and Malaysia, with secondary centers in surrounding areas. Novel and commercially ...

Cucumber gene list 2017

USDA-ARS?s Scientific Manuscript database

This is an update of the 2010 version of Cucumber Gene List. Since the release of the cucumber draft genome in 2009, significant progress has been made in developing cucumber genetic and genomics resources. A number of genes or QTLs have been tagged with molecular markers, which provides us a better...

Emerging crops in the USDA arid lands germplasm collection

USDA-ARS?s Scientific Manuscript database

The USDA National Plant Germplasm System maintains collections of several emerging crops for arid lands at the National Arid Land Plant Genetic Resources Unit in Parlier, CA (NALPGRU). The guayule, jojoba, and prickly pear collections are most active in terms of current research and crop development...

Developing Single Nucleotide Polymorphism markers for the identification of Coffee germplasm

USDA-ARS?s Scientific Manuscript database

Coffee is one of the most widely consumed beverages that represent a multibillion dollar global industry. Accurate identification of coffee cultivars is essential for efficient management, exchange and use of coffee genetic resources. So far a universal platform that can allow data comparison across...

Genetic and developing genomic resources in black raspberry

USDA-ARS?s Scientific Manuscript database

Over the last 75 years, the black raspberry industry in the United States has steadily declined due to lack of adapted and disease resistant cultivars. The high anthocyanin content of black raspberry and associated health benefits have revived interest in production and breeding new cultivars. The U...

Developing genetic and genomic resources in black raspberry

USDA-ARS?s Scientific Manuscript database

Over the last 75 years, the black raspberry industry in the United States has steadily declined due to lack of adapted and disease resistant cultivars. The high anthocyanin content of black raspberry and associated health benefits have revived interest in production and breeding new cultivars. The ...

[EST-SSR identification, markers development of Ligusticum chuanxiong based on Ligusticum chuanxiong transcriptome sequences].

PubMed

Yuan, Can; Peng, Fang; Yang, Ze-Mao; Zhong, Wen-Juan; Mou, Fang-Sheng; Gong, Yi-Yun; Ji, Pei-Cheng; Pu, De-Qiang; Huang, Hai-Yan; Yang, Xiao; Zhang, Chao

2017-09-01

Ligusticum chuanxiong is a well-known traditional Chinese medicine plant. The study on its molecular markers development and germplasm resources is very important. In this study, we obtained 24 422 unigenes by assembling transcriptome sequencing reads of L. chuanxiong root. EST-SSR was detected and 4 073 SSR loci were identified. EST-SSR distribution and characteristic analysis results showed that the mono-nucleotide repeats were the main repeat types, accounting for 41.0%. In addition, the sequences containing SSR were functionally annotated in Gene Ontology (GO) and KEGG pathway and were assigned to 49 GO categories, 242 KEGG pathways, among them 2 201 sequences were annotated against Nr database. By validating 235 EST-SSRs,74 primer pairs were ultimately proved to have high quality amplification. Subsequently, genetic diversity analysis, UPGMA cluster analysis, PCoA analysis and population structure analysis of 34 L. chuanxiong germplasm resources were carried out with 74 primer pairs. In both UPGMA tree and PCoA results, L. chuanxiong resources were clustered into two groups, which are believed to be partial related to their geographical distribution. In this study, EST-SSRs in L. chuanxiong was firstly identified, and newly developed molecular markers would contribute significantly to further genetic diversity study, the purity detection, gene mapping, and molecular breeding. Copyright© by the Chinese Pharmaceutical Association.

Genetics Evaluation Guidelines for the Etiologic Diagnosis of Congenital Hearing Loss

PubMed Central

2002-01-01

The advent of hearing screening in newborns in many states has led to an increase in the use of genetic testing and related genetic services in the follow-up of infants with hearing loss. A significant proportion of those with congenital hearing loss have genetic etiologies underlying their hearing loss. To ensure that those identified with congenital hearing loss receive the genetic services appropriate to their conditions, the Maternal and Child Health Bureau of the Health Resources and Services Administration funded the American College of Medical Genetics to convene an expert panel to develop guidelines for the genetic evaluation of congential hearing loss. After a brief overview of the current knowledge of hearing loss, newborn screening, and newborn hearing screening, we provide an overview of genetic services and a guideline that describes how best to ensure that patients receive appropriate genetic services. The significant contribution of genetic factors to these conditions combined with the rapid evolution of knowledge about the genetics of these conditions overlaid with the inherently multidisciplinary nature of genetic services provides an example of a condition for which a well-integrated multidisciplinary approach to care is clearly needed. PMID:12180152

Pediatric Genomic Data Inventory (PGDI) Overview

Cancer.gov

About Pediatric cancer is a genetic disease that can largely differ from similar malignancies in an adult population. To fuel new discoveries and treatments specific to pediatric oncologies, the NCI Office of Cancer Genomics has developed a dynamic resource known as the Pediatric Genomic Data Inventory to allow investigators to more easily locate genomic datasets. This resource lists known ongoing and completed sequencing projects of pediatric cancer cohorts from the United States and other countries, along with some basic details and reference metadata.

Effect of genetic European taurine ancestry on milk yield of Ankole-Holstein crossbred dairy cattle in mixed smallholders system of Burundi highlands.

PubMed

Manirakiza, J; Hatungumukama, G; Thévenon, S; Gautier, M; Besbes, B; Flori, L; Detilleux, J

2017-10-01

Different breeding systems associated with specific bovine genetic resources have coexisted in Burundi. To prepare for the development of a national action plan for the improvement of bovine genetic resources in Burundi, we aimed at performing genetic characterization of Ankole and Ankole × European crossbred individuals and assessing the effect of European ancestry on milk productivity of cows kept under the mixed crops livestock system. To that end, we genotyped 37 Ankole and 138 crossbred individuals on 42 636 SNPs and combined these genotypes with those from 21 cattle breeds, representative of the bovine genetic diversity. We also measured milk yield not suckled and estimated suckled milk. Given the results, we confirmed the indicine × African taurine admixed origin of the Ankole in Burundi and showed that crossbred individuals present a high proportion of European ancestry (i.e. 57% on average). As the proportion of European ancestry increased, milk yield increased by 0.03 ± 0.01 l/day, at a lower extent than expected. We also observed that breeders were unable to correctly evaluate the European proportion in their livestock. Our results may provide useful information for objective dairy breeding in Burundi. As an example, an ex-situ conservation program of Ankole within the framework of value chains is proposed as an accompanying strategy to improve the sustainability of the crossbreeding program. © 2017 Stichting International Foundation for Animal Genetics.

Statistical genetics concepts and approaches in schizophrenia and related neuropsychiatric research.

PubMed

Schork, Nicholas J; Greenwood, Tiffany A; Braff, David L

2007-01-01

Statistical genetics is a research field that focuses on mathematical models and statistical inference methodologies that relate genetic variations (ie, naturally occurring human DNA sequence variations or "polymorphisms") to particular traits or diseases (phenotypes) usually from data collected on large samples of families or individuals. The ultimate goal of such analysis is the identification of genes and genetic variations that influence disease susceptibility. Although of extreme interest and importance, the fact that many genes and environmental factors contribute to neuropsychiatric diseases of public health importance (eg, schizophrenia, bipolar disorder, and depression) complicates relevant studies and suggests that very sophisticated mathematical and statistical modeling may be required. In addition, large-scale contemporary human DNA sequencing and related projects, such as the Human Genome Project and the International HapMap Project, as well as the development of high-throughput DNA sequencing and genotyping technologies have provided statistical geneticists with a great deal of very relevant and appropriate information and resources. Unfortunately, the use of these resources and their interpretation are not straightforward when applied to complex, multifactorial diseases such as schizophrenia. In this brief and largely nonmathematical review of the field of statistical genetics, we describe many of the main concepts, definitions, and issues that motivate contemporary research. We also provide a discussion of the most pressing contemporary problems that demand further research if progress is to be made in the identification of genes and genetic variations that predispose to complex neuropsychiatric diseases.

SZDB: A Database for Schizophrenia Genetic Research

PubMed Central

Wu, Yong; Yao, Yong-Gang

2017-01-01

Abstract Schizophrenia (SZ) is a debilitating brain disorder with a complex genetic architecture. Genetic studies, especially recent genome-wide association studies (GWAS), have identified multiple variants (loci) conferring risk to SZ. However, how to efficiently extract meaningful biological information from bulk genetic findings of SZ remains a major challenge. There is a pressing need to integrate multiple layers of data from various sources, eg, genetic findings from GWAS, copy number variations (CNVs), association and linkage studies, gene expression, protein–protein interaction (PPI), co-expression, expression quantitative trait loci (eQTL), and Encyclopedia of DNA Elements (ENCODE) data, to provide a comprehensive resource to facilitate the translation of genetic findings into SZ molecular diagnosis and mechanism study. Here we developed the SZDB database (http://www.szdb.org/), a comprehensive resource for SZ research. SZ genetic data, gene expression data, network-based data, brain eQTL data, and SNP function annotation information were systematically extracted, curated and deposited in SZDB. In-depth analyses and systematic integration were performed to identify top prioritized SZ genes and enriched pathways. Multiple types of data from various layers of SZ research were systematically integrated and deposited in SZDB. In-depth data analyses and integration identified top prioritized SZ genes and enriched pathways. We further showed that genes implicated in SZ are highly co-expressed in human brain and proteins encoded by the prioritized SZ risk genes are significantly interacted. The user-friendly SZDB provides high-confidence candidate variants and genes for further functional characterization. More important, SZDB provides convenient online tools for data search and browse, data integration, and customized data analyses. PMID:27451428

Broad-Scale Genetic Diversity of Cannabis for Forensic Applications.

PubMed

Dufresnes, Christophe; Jan, Catherine; Bienert, Friederike; Goudet, Jérôme; Fumagalli, Luca

2017-01-01

Cannabis (hemp and marijuana) is an iconic yet controversial crop. On the one hand, it represents a growing market for pharmaceutical and agricultural sectors. On the other hand, plants synthesizing the psychoactive THC produce the most widespread illicit drug in the world. Yet, the difficulty to reliably distinguish between Cannabis varieties based on morphological or biochemical criteria impedes the development of promising industrial programs and hinders the fight against narcotrafficking. Genetics offers an appropriate alternative to characterize drug vs. non-drug Cannabis. However, forensic applications require rapid and affordable genotyping of informative and reliable molecular markers for which a broad-scale reference database, representing both intra- and inter-variety variation, is available. Here we provide such a resource for Cannabis, by genotyping 13 microsatellite loci (STRs) in 1 324 samples selected specifically for fibre (24 hemp varieties) and drug (15 marijuana varieties) production. We showed that these loci are sufficient to capture most of the genome-wide diversity patterns recently revealed by NGS data. We recovered strong genetic structure between marijuana and hemp and demonstrated that anonymous samples can be confidently assigned to either plant types. Fibres appear genetically homogeneous whereas drugs show low (often clonal) diversity within varieties, but very high genetic differentiation between them, likely resulting from breeding practices. Based on an additional test dataset including samples from 41 local police seizures, we showed that the genetic signature of marijuana cultivars could be used to trace crime scene evidence. To date, our study provides the most comprehensive genetic resource for Cannabis forensics worldwide.

Broad-Scale Genetic Diversity of Cannabis for Forensic Applications

PubMed Central

Dufresnes, Christophe; Jan, Catherine; Bienert, Friederike; Goudet, Jérôme; Fumagalli, Luca

2017-01-01

Cannabis (hemp and marijuana) is an iconic yet controversial crop. On the one hand, it represents a growing market for pharmaceutical and agricultural sectors. On the other hand, plants synthesizing the psychoactive THC produce the most widespread illicit drug in the world. Yet, the difficulty to reliably distinguish between Cannabis varieties based on morphological or biochemical criteria impedes the development of promising industrial programs and hinders the fight against narcotrafficking. Genetics offers an appropriate alternative to characterize drug vs. non-drug Cannabis. However, forensic applications require rapid and affordable genotyping of informative and reliable molecular markers for which a broad-scale reference database, representing both intra- and inter-variety variation, is available. Here we provide such a resource for Cannabis, by genotyping 13 microsatellite loci (STRs) in 1 324 samples selected specifically for fibre (24 hemp varieties) and drug (15 marijuana varieties) production. We showed that these loci are sufficient to capture most of the genome-wide diversity patterns recently revealed by NGS data. We recovered strong genetic structure between marijuana and hemp and demonstrated that anonymous samples can be confidently assigned to either plant types. Fibres appear genetically homogeneous whereas drugs show low (often clonal) diversity within varieties, but very high genetic differentiation between them, likely resulting from breeding practices. Based on an additional test dataset including samples from 41 local police seizures, we showed that the genetic signature of marijuana cultivars could be used to trace crime scene evidence. To date, our study provides the most comprehensive genetic resource for Cannabis forensics worldwide. PMID:28107530

Cryopreservation of eucalyptus genetic resources

USDA-ARS?s Scientific Manuscript database

The long-term preservation of forest genetic resources is a vital part of preserving our forest crops for future generations. Unfortunately there are few genebanks dedicated to forest trees and very few methods aside from field plantings of germplasm collections of elite clonal individuals. The use ...

Human Ageing Genomic Resources: Integrated databases and tools for the biology and genetics of ageing

PubMed Central

Tacutu, Robi; Craig, Thomas; Budovsky, Arie; Wuttke, Daniel; Lehmann, Gilad; Taranukha, Dmitri; Costa, Joana; Fraifeld, Vadim E.; de Magalhães, João Pedro

2013-01-01

The Human Ageing Genomic Resources (HAGR, http://genomics.senescence.info) is a freely available online collection of research databases and tools for the biology and genetics of ageing. HAGR features now several databases with high-quality manually curated data: (i) GenAge, a database of genes associated with ageing in humans and model organisms; (ii) AnAge, an extensive collection of longevity records and complementary traits for >4000 vertebrate species; and (iii) GenDR, a newly incorporated database, containing both gene mutations that interfere with dietary restriction-mediated lifespan extension and consistent gene expression changes induced by dietary restriction. Since its creation about 10 years ago, major efforts have been undertaken to maintain the quality of data in HAGR, while further continuing to develop, improve and extend it. This article briefly describes the content of HAGR and details the major updates since its previous publications, in terms of both structure and content. The completely redesigned interface, more intuitive and more integrative of HAGR resources, is also presented. Altogether, we hope that through its improvements, the current version of HAGR will continue to provide users with the most comprehensive and accessible resources available today in the field of biogerontology. PMID:23193293

Knowledge discovery through games and game theory

NASA Astrophysics Data System (ADS)

Smith, James F., III; Rhyne, Robert D.

2001-03-01

A fuzzy logic based expert system has been developed that automatically allocates electronic attack (EA) resources in real-time over many dissimilar platforms. The platforms can be very general, e.g., ships, planes, robots, land based facilities, etc. Potential foes the platforms deal with can also be general. The initial version of the algorithm was optimized using a genetic algorithm employing fitness functions constructed based on expertise. A new approach is being explored that involves embedding the resource manager in a electronic game environment. The game allows a human expert to play against the resource manager in a simulated battlespace with each of the defending platforms being exclusively directed by the fuzzy resource manager and the attacking platforms being controlled by the human expert or operating autonomously under their own logic. This approach automates the data mining problem. The game automatically creates a database reflecting the domain expert's knowledge, it calls a data mining function, a genetic algorithm, for data mining of the database as required. The game allows easy evaluation of the information mined in the second step. The measure of effectiveness (MOE) for re-optimization is discussed. The mined information is extremely valuable as shown through demanding scenarios.

Genetics Home Reference: myasthenia gravis

MedlinePlus

... ventilation assistance. This respiratory failure, called a myasthenic crisis, may be triggered by stresses such as infections ... be inherited? More about Inheriting Genetic Conditions Diagnosis & Management Resources Genetic Testing (2 links) Genetic Testing Registry: ...

Genetics Home Reference: hereditary angioedema

MedlinePlus

... 000 people. Type I is the most common, accounting for 85 percent of cases. Type II occurs ... be inherited? More about Inheriting Genetic Conditions Diagnosis & Management Resources Genetic Testing (3 links) Genetic Testing Registry: ...

Genetics Home Reference: multiminicore disease

MedlinePlus

... are less common than the classic form, together accounting for about 25 percent of all cases. The ... be inherited? More about Inheriting Genetic Conditions Diagnosis & Management Resources Genetic Testing (5 links) Genetic Testing Registry: ...

"Touching Triton": Building Student Understanding of Complex Disease Risk.

PubMed

Loftin, Madelene; East, Kelly; Hott, Adam; Lamb, Neil

2016-01-01

Life science classrooms often emphasize the exception to the rule when it comes to teaching genetics, focusing heavily on rare single-gene and Mendelian traits. By contrast, the vast majority of human traits and diseases are caused by more complicated interactions between genetic and environmental factors. Research indicates that students have a deterministic view of genetics, generalize Mendelian inheritance patterns to all traits, and have unrealistic expectations of genetic technologies. The challenge lies in how to help students analyze complex disease risk with a lack of curriculum materials. Providing open access to both content resources and an engaging storyline can be achieved using a "serious game" model. "Touching Triton" was developed as a serious game in which students are asked to analyze data from a medical record, family history, and genomic report in order to develop an overall lifetime risk estimate of six common, complex diseases. Evaluation of student performance shows significant learning gains in key content areas along with a high level of engagement.

Developing single nucleotide polymorphism (SNP) markers from transcriptome sequences for identification of longan (Dimocarpus longan) germplasm

PubMed Central

Wang, Boyi; Tan, Hua-Wei; Fang, Wanping; Meinhardt, Lyndel W; Mischke, Sue; Matsumoto, Tracie; Zhang, Dapeng

2015-01-01

Longan (Dimocarpus longan Lour.) is an important tropical fruit tree crop. Accurate varietal identification is essential for germplasm management and breeding. Using longan transcriptome sequences from public databases, we developed single nucleotide polymorphism (SNP) markers; validated 60 SNPs in 50 longan germplasm accessions, including cultivated varieties and wild germplasm; and designated 25 SNP markers that unambiguously identified all tested longan varieties with high statistical rigor (P<0.0001). Multiple trees from the same clone were verified and off-type trees were identified. Diversity analysis revealed genetic relationships among analyzed accessions. Cultivated varieties differed significantly from wild populations (Fst=0.300; P<0.001), demonstrating untapped genetic diversity for germplasm conservation and utilization. Within cultivated varieties, apparent differences between varieties from China and those from Thailand and Hawaii indicated geographic patterns of genetic differentiation. These SNP markers provide a powerful tool to manage longan genetic resources and breeding, with accurate and efficient genotype identification. PMID:26504559

Development of genic-SSR markers by deep transcriptome sequencing in pigeonpea [Cajanus cajan (L.) Millspaugh].

PubMed

Dutta, Sutapa; Kumawat, Giriraj; Singh, Bikram P; Gupta, Deepak K; Singh, Sangeeta; Dogra, Vivek; Gaikwad, Kishor; Sharma, Tilak R; Raje, Ranjeet S; Bandhopadhya, Tapas K; Datta, Subhojit; Singh, Mahendra N; Bashasab, Fakrudin; Kulwal, Pawan; Wanjari, K B; K Varshney, Rajeev; Cook, Douglas R; Singh, Nagendra K

2011-01-20

Pigeonpea [Cajanus cajan (L.) Millspaugh], one of the most important food legumes of semi-arid tropical and subtropical regions, has limited genomic resources, particularly expressed sequence based (genic) markers. We report a comprehensive set of validated genic simple sequence repeat (SSR) markers using deep transcriptome sequencing, and its application in genetic diversity analysis and mapping. In this study, 43,324 transcriptome shotgun assembly unigene contigs were assembled from 1.696 million 454 GS-FLX sequence reads of separate pooled cDNA libraries prepared from leaf, root, stem and immature seed of two pigeonpea varieties, Asha and UPAS 120. A total of 3,771 genic-SSR loci, excluding homopolymeric and compound repeats, were identified; of which 2,877 PCR primer pairs were designed for marker development. Dinucleotide was the most common repeat motif with a frequency of 60.41%, followed by tri- (34.52%), hexa- (2.62%), tetra- (1.67%) and pentanucleotide (0.76%) repeat motifs. Primers were synthesized and tested for 772 of these loci with repeat lengths of ≥ 18 bp. Of these, 550 markers were validated for consistent amplification in eight diverse pigeonpea varieties; 71 were found to be polymorphic on agarose gel electrophoresis. Genetic diversity analysis was done on 22 pigeonpea varieties and eight wild species using 20 highly polymorphic genic-SSR markers. The number of alleles at these loci ranged from 4-10 and the polymorphism information content values ranged from 0.46 to 0.72. Neighbor-joining dendrogram showed distinct separation of the different groups of pigeonpea cultivars and wild species. Deep transcriptome sequencing of the two parental lines helped in silico identification of polymorphic genic-SSR loci to facilitate the rapid development of an intra-species reference genetic map, a subset of which was validated for expected allelic segregation in the reference mapping population. We developed 550 validated genic-SSR markers in pigeonpea using deep transcriptome sequencing. From these, 20 highly polymorphic markers were used to evaluate the genetic relationship among species of the genus Cajanus. A comprehensive set of genic-SSR markers was developed as an important genomic resource for diversity analysis and genetic mapping in pigeonpea.

Development of genic-SSR markers by deep transcriptome sequencing in pigeonpea [Cajanus cajan (L.) Millspaugh

PubMed Central

2011-01-01

Background Pigeonpea [Cajanus cajan (L.) Millspaugh], one of the most important food legumes of semi-arid tropical and subtropical regions, has limited genomic resources, particularly expressed sequence based (genic) markers. We report a comprehensive set of validated genic simple sequence repeat (SSR) markers using deep transcriptome sequencing, and its application in genetic diversity analysis and mapping. Results In this study, 43,324 transcriptome shotgun assembly unigene contigs were assembled from 1.696 million 454 GS-FLX sequence reads of separate pooled cDNA libraries prepared from leaf, root, stem and immature seed of two pigeonpea varieties, Asha and UPAS 120. A total of 3,771 genic-SSR loci, excluding homopolymeric and compound repeats, were identified; of which 2,877 PCR primer pairs were designed for marker development. Dinucleotide was the most common repeat motif with a frequency of 60.41%, followed by tri- (34.52%), hexa- (2.62%), tetra- (1.67%) and pentanucleotide (0.76%) repeat motifs. Primers were synthesized and tested for 772 of these loci with repeat lengths of ≥18 bp. Of these, 550 markers were validated for consistent amplification in eight diverse pigeonpea varieties; 71 were found to be polymorphic on agarose gel electrophoresis. Genetic diversity analysis was done on 22 pigeonpea varieties and eight wild species using 20 highly polymorphic genic-SSR markers. The number of alleles at these loci ranged from 4-10 and the polymorphism information content values ranged from 0.46 to 0.72. Neighbor-joining dendrogram showed distinct separation of the different groups of pigeonpea cultivars and wild species. Deep transcriptome sequencing of the two parental lines helped in silico identification of polymorphic genic-SSR loci to facilitate the rapid development of an intra-species reference genetic map, a subset of which was validated for expected allelic segregation in the reference mapping population. Conclusion We developed 550 validated genic-SSR markers in pigeonpea using deep transcriptome sequencing. From these, 20 highly polymorphic markers were used to evaluate the genetic relationship among species of the genus Cajanus. A comprehensive set of genic-SSR markers was developed as an important genomic resource for diversity analysis and genetic mapping in pigeonpea. PMID:21251263

Genetics Home Reference: Gillespie syndrome

MedlinePlus

... the prognosis of a genetic condition? Genetic and Rare Diseases Information Center Frequency The prevalence of Gillespie syndrome ... Developmental Disabilities Health Topic: Eye Diseases Genetic and Rare Diseases Information Center (1 link) Gillespie syndrome Educational Resources ( ...

Genetics Home Reference: combined pituitary hormone deficiency

MedlinePlus

... the most common known cause of this disorder, accounting for an estimated 12 to 55 percent of ... be inherited? More about Inheriting Genetic Conditions Diagnosis & Management Resources Genetic Testing (7 links) Genetic Testing Registry: ...

Genetics Home Reference: familial isolated pituitary adenoma

MedlinePlus

... 1,000 people. FIPA, though, is quite rare, accounting for approximately 2 percent of pituitary adenomas. More ... be inherited? More about Inheriting Genetic Conditions Diagnosis & Management Resources Genetic Testing (1 link) Genetic Testing Registry: ...

Role of genomics in promoting the utilization of plant genetic resources in genebanks

PubMed Central

Wambugu, Peterson W; Ndjiondjop, Marie-Noelle

2018-01-01

Abstract Global efforts have seen the world’s plant genetic resources (PGRs) conserved in about 1625 germ plasm repositories. Utility of these resources is important in increasing the resilience and productivity of agricultural production systems. However, despite their importance, utility of these resources has been poor. This article reviews the real and potential application of the current advances in genomic technologies in improving the utilization of these resources. The actual and potential application of these genomic approaches in plant identification, phylogenetic analysis, analysing the genetic value of germ plasm, facilitating germ plasm selection in genebanks as well as instilling confidence in international germ plasm exchange system is discussed. We note that if genebanks are to benefit from this genomic revolution, there is need for fundamental changes in the way genebanks are managed, perceived, organized and funded. Increased collaboration between genebank managers and the user community is also recommended PMID:29688255

Complex Genetics of Behavior: BXDs in the Automated Home-Cage.

PubMed

Loos, Maarten; Verhage, Matthijs; Spijker, Sabine; Smit, August B

2017-01-01

This chapter describes a use case for the genetic dissection and automated analysis of complex behavioral traits using the genetically diverse panel of BXD mouse recombinant inbred strains. Strains of the BXD resource differ widely in terms of gene and protein expression in the brain, as well as in their behavioral repertoire. A large mouse resource opens the possibility for gene finding studies underlying distinct behavioral phenotypes, however, such a resource poses a challenge in behavioral phenotyping. To address the specifics of large-scale screening we describe how to investigate: (1) how to assess mouse behavior systematically in addressing a large genetic cohort, (2) how to dissect automation-derived longitudinal mouse behavior into quantitative parameters, and (3) how to map these quantitative traits to the genome, deriving loci underlying aspects of behavior.

Analysis of BAC-end sequences (BESs) and development of BES-SSR markers for genetic mapping and hybrid purity assessment in pigeonpea (Cajanus spp.)

PubMed Central

2011-01-01

Background Pigeonpea [Cajanus cajan (L.) Millsp.] is an important legume crop of rainfed agriculture. Despite of concerted research efforts directed to pigeonpea improvement, stagnated productivity of pigeonpea during last several decades may be accounted to prevalence of various biotic and abiotic constraints and the situation is exacerbated by availability of inadequate genomic resources to undertake any molecular breeding programme for accelerated crop improvement. With the objective of enhancing genomic resources for pigeonpea, this study reports for the first time, large scale development of SSR markers from BAC-end sequences and their subsequent use for genetic mapping and hybridity testing in pigeonpea. Results A set of 88,860 BAC (bacterial artificial chromosome)-end sequences (BESs) were generated after constructing two BAC libraries by using HindIII (34,560 clones) and BamHI (34,560 clones) restriction enzymes. Clustering based on sequence identity of BESs yielded a set of >52K non-redundant sequences, comprising 35 Mbp or >4% of the pigeonpea genome. These sequences were analyzed to develop annotation lists and subdivide the BESs into genome fractions (e.g., genes, retroelements, transpons and non-annotated sequences). Parallel analysis of BESs for microsatellites or simple sequence repeats (SSRs) identified 18,149 SSRs, from which a set of 6,212 SSRs were selected for further analysis. A total of 3,072 novel SSR primer pairs were synthesized and tested for length polymorphism on a set of 22 parental genotypes of 13 mapping populations segregating for traits of interest. In total, we identified 842 polymorphic SSR markers that will have utility in pigeonpea improvement. Based on these markers, the first SSR-based genetic map comprising of 239 loci was developed for this previously uncharacterized genome. Utility of developed SSR markers was also demonstrated by identifying a set of 42 markers each for two hybrids (ICPH 2671 and ICPH 2438) for genetic purity assessment in commercial hybrid breeding programme. Conclusion In summary, while BAC libraries and BESs should be useful for genomics studies, BES-SSR markers, and the genetic map should be very useful for linking the genetic map with a future physical map as well as for molecular breeding in pigeonpea. PMID:21447154

Recommendations for developing and applying genetic tools to assess and manage biological invasions in marine ecosystems

EPA Science Inventory

The European Union’s Marine Strategy Framework Directive (MSFD) aims to adopt integrated ecosystem management approaches to achieve or maintain “Good Environmental Status” for marine waters, habitats and resources, including mitigation of the negative effects of non-indigenous sp...

The eastern oyster genome: A resource for comparative genomics in shellfish aquaculture species

USDA-ARS?s Scientific Manuscript database

Oyster aquaculture is an important sector of world food production. As such, it is imperative to develop a high quality reference genome for the eastern oyster, Crassostrea virginica, to assist in the elucidation of the genomic basis of commercially important traits. All genetic, gene expression and...

Developing germplasm resources to identify the genetic basis of resistance to common scab in potato

USDA-ARS?s Scientific Manuscript database

Common scab, caused mainly by the soil-borne bacterium Streptomyces scabies, produces lesions on potato tubers, reducing tuber quality and profitability. Methods to manage common scab are often expensive, impractical, and can be ineffective. Therefore, creating cultivars that are resistant to common...

Biotechnology Education and the Internet. ERIC Digest.

ERIC Educational Resources Information Center

Lee, Thomas

The world of modern biotechnology is based on recent developments in molecular biology, especially those in genetic engineering. Since this is a relatively new and rapidly advancing field of study, there are few traditional sources of information and activities. This digest highlights biotechnology resources including those that can be found on…

Development of a high-density cranberry SSR linkage map for comparative genetic analysis and trait detection

USDA-ARS?s Scientific Manuscript database

Since its domestication 200 years ago, breeding of the American Cranberry (Vaccinium macrocarpon) has relied on phenotypic selection because applicable resources for molecular improvement strategies such as marker-assisted selection (MAS) remain limited. To enable MAS in cranberry, the first high de...

Growth medium alterations improve in vitro cold storage of pear germplasm

USDA-ARS?s Scientific Manuscript database

Development of new fruit cultivars is dependent on genetic resource collections such as those at the Pomological Garden at the Institute of Horticulture and Viticulture near Almaty, Kazakhstan. The pear germplasm collection of the Pomological Garden contains 615 cultivars and 3 species. About 36 ac...

Genetic characterization of the soybean Nested Association Mapping (NAM) population

USDA-ARS?s Scientific Manuscript database

A population of nested association mapping (NAM) families can be a valuable resource to a research community. A set of NAM families were developed by crossing 40 diverse soybean genotypes to the common hub cultivar IA 3023. The 41 parents were sequenced with next generation sequencing for single nuc...

Parallel Curriculum Units for Science, Grades 6-12

ERIC Educational Resources Information Center

Leppien, Jann H.; Purcell, Jeanne H.

2011-01-01

Based on the best-selling book "The Parallel Curriculum", this professional development resource gives multifaceted examples of rigorous learning opportunities for science students in Grades 6-12. The four sample units revolve around genetics, the convergence of science and society, the integration of language arts and biology, and the periodic…

Persian walnut breeding in California

Treesearch

Charles A. Leslie; Gale H. McGranahan

2004-01-01

For over 50 years the University of California Davis Walnut Breeding Program has worked to address the needs of California walnut growers by identifying genetic approaches to problems and developing improved cultivars. The breeding program is a cooperative endeavor that draws on the efforts and resources of university researchers and facilities, USDA germplasm programs...

High-throughput RAD-SNP genotyping for characterization of sugar beet genotypes

USDA-ARS?s Scientific Manuscript database

High-throughput SNP genotyping provides a rapid way of developing resourceful set of markers for delineating the genetic architecture and for effective species discrimination. In the presented research, we demonstrate a set of 192 SNPs for effective genotyping in sugar beet using high-throughput mar...

A portable expression resource for engineering cross-species genetic circuits and pathways

PubMed Central

Kushwaha, Manish; Salis, Howard M.

2015-01-01

Genetic circuits and metabolic pathways can be reengineered to allow organisms to process signals and manufacture useful chemicals. However, their functions currently rely on organism-specific regulatory parts, fragmenting synthetic biology and metabolic engineering into host-specific domains. To unify efforts, here we have engineered a cross-species expression resource that enables circuits and pathways to reuse the same genetic parts, while functioning similarly across diverse organisms. Our engineered system combines mixed feedback control loops and cross-species translation signals to autonomously self-regulate expression of an orthogonal polymerase without host-specific promoters, achieving nontoxic and tuneable gene expression in diverse Gram-positive and Gram-negative bacteria. Combining 50 characterized system variants with mechanistic modelling, we show how the cross-species expression resource's dynamics, capacity and toxicity are controlled by the control loops' architecture and feedback strengths. We also demonstrate one application of the resource by reusing the same genetic parts to express a biosynthesis pathway in both model and non-model hosts. PMID:26184393

MiSNPDb: a web-based genomic resources of tropical ecology fruit mango (Mangifera indica L.) for phylogeography and varietal differentiation.

PubMed

Iquebal, M A; Jaiswal, Sarika; Mahato, Ajay Kumar; Jayaswal, Pawan K; Angadi, U B; Kumar, Neeraj; Sharma, Nimisha; Singh, Anand K; Srivastav, Manish; Prakash, Jai; Singh, S K; Khan, Kasim; Mishra, Rupesh K; Rajan, Shailendra; Bajpai, Anju; Sandhya, B S; Nischita, Puttaraju; Ravishankar, K V; Dinesh, M R; Rai, Anil; Kumar, Dinesh; Sharma, Tilak R; Singh, Nagendra K

2017-11-02

Mango is one of the most important fruits of tropical ecological region of the world, well known for its nutritive value, aroma and taste. Its world production is >45MT worth >200 billion US dollars. Genomic resources are required for improvement in productivity and management of mango germplasm. There is no web-based genomic resources available for mango. Hence rapid and cost-effective high throughput putative marker discovery is required to develop such resources. RAD-based marker discovery can cater this urgent need till whole genome sequence of mango becomes available. Using a panel of 84 mango varieties, a total of 28.6 Gb data was generated by ddRAD-Seq approach on Illumina HiSeq 2000 platform. A total of 1.25 million SNPs were discovered. Phylogenetic tree using 749 common SNPs across these varieties revealed three major lineages which was compared with geographical locations. A web genomic resources MiSNPDb, available at http://webtom.cabgrid.res.in/mangosnps/ is based on 3-tier architecture, developed using PHP, MySQL and Javascript. This web genomic resources can be of immense use in the development of high density linkage map, QTL discovery, varietal differentiation, traceability, genome finishing and SNP chip development for future GWAS in genomic selection program. We report here world's first web-based genomic resources for genetic improvement and germplasm management of mango.

The First Genetic Map in Sweet Osmanthus (Osmanthus fragrans Lour.) Using Specific Locus Amplified Fragment Sequencing

PubMed Central

He, Yanxia; Yuan, Wangjun; Dong, Meifang; Han, Yuanji; Shang, Fude

2017-01-01

Osmanthus fragrans is an ornamental plant of substantial commercial value, and no genetic linkage maps of this species have previously been reported. Specific-locus amplified fragment sequencing (SLAF-seq) is a recently developed technology that allows massive single nucleotide polymorphisms (SNPs) to be identified and high-resolution genotyping. In our current research, we generated the first genetic map of O. fragrans using SLAF-seq, which is composed with 206.92 M paired-end reads and 173,537 SLAF markers. Among total 90,715 polymorphic SLAF markers, 15,317 polymorphic SLAFs could be used for genetic map construction. The integrated map contained 14,189 high quality SLAFs that were grouped in 23 genetic linkage groups, with a total length of 2962.46 cM and an average distance of 0.21 cM between two adjacent markers. In addition, 23,664 SNPs were identified from the mapped markers. As far as we know, this is the first of the genetic map of O. fragrans. Our results are further demonstrate that SLAF-seq is a very effective method for developing markers and constructing high-density linkage maps. The SNP markers and the genetic map reported in this study should be valuable resource in future research. PMID:29018460

A genome resource to address mechanisms of developmental programming: determination of the fetal sheep heart transcriptome.

PubMed

Cox, Laura A; Glenn, Jeremy P; Spradling, Kimberly D; Nijland, Mark J; Garcia, Roy; Nathanielsz, Peter W; Ford, Stephen P

2012-06-15

The pregnant sheep has provided seminal insights into reproduction related to animal and human development (ovarian function, fertility, implantation, fetal growth, parturition and lactation). Fetal sheep physiology has been extensively studied since 1950, contributing significantly to the basis for our understanding of many aspects of fetal development and behaviour that remain in use in clinical practice today. Understanding mechanisms requires the combination of systems approaches uniquely available in fetal sheep with the power of genomic studies. Absence of the full range of sheep genomic resources has limited the full realization of the power of this model, impeding progress in emerging areas of pregnancy biology such as developmental programming. We have examined the expressed fetal sheep heart transcriptome using high-throughput sequencing technologies. In so doing we identified 36,737 novel transcripts and describe genes, gene variants and pathways relevant to fundamental developmental mechanisms. Genes with the highest expression levels and with novel exons in the fetal heart transcriptome are known to play central roles in muscle development. We show that high-throughput sequencing methods can generate extensive transcriptome information in the absence of an assembled and annotated genome for that species. The gene sequence data obtained provide a unique genomic resource for sheep specific genetic technology development and, combined with the polymorphism data, augment annotation and assembly of the sheep genome. In addition, identification and pathway analysis of novel fetal sheep heart transcriptome splice variants is a first step towards revealing mechanisms of genetic variation and gene environment interactions during fetal heart development.

A genome resource to address mechanisms of developmental programming: determination of the fetal sheep heart transcriptome

PubMed Central

Cox, Laura A; Glenn, Jeremy P; Spradling, Kimberly D; Nijland, Mark J; Garcia, Roy; Nathanielsz, Peter W; Ford, Stephen P

2012-01-01

The pregnant sheep has provided seminal insights into reproduction related to animal and human development (ovarian function, fertility, implantation, fetal growth, parturition and lactation). Fetal sheep physiology has been extensively studied since 1950, contributing significantly to the basis for our understanding of many aspects of fetal development and behaviour that remain in use in clinical practice today. Understanding mechanisms requires the combination of systems approaches uniquely available in fetal sheep with the power of genomic studies. Absence of the full range of sheep genomic resources has limited the full realization of the power of this model, impeding progress in emerging areas of pregnancy biology such as developmental programming. We have examined the expressed fetal sheep heart transcriptome using high-throughput sequencing technologies. In so doing we identified 36,737 novel transcripts and describe genes, gene variants and pathways relevant to fundamental developmental mechanisms. Genes with the highest expression levels and with novel exons in the fetal heart transcriptome are known to play central roles in muscle development. We show that high-throughput sequencing methods can generate extensive transcriptome information in the absence of an assembled and annotated genome for that species. The gene sequence data obtained provide a unique genomic resource for sheep specific genetic technology development and, combined with the polymorphism data, augment annotation and assembly of the sheep genome. In addition, identification and pathway analysis of novel fetal sheep heart transcriptome splice variants is a first step towards revealing mechanisms of genetic variation and gene environment interactions during fetal heart development. PMID:22508961

Permanent Genetic Resources added to Molecular Ecology Resources Database 1 October 2011 – 30 November 2011

PubMed Central

ABREU, ALUANA G.; ALBAINA, A.; ALPERMANN, TILMAN J.; APKENAS, VANESSA E.; BANKHEAD-DRONNET, S.; BERGEK, SARA; BERUMEN, MICHAEL L.; CHO, CHANG-HUNG; CLOBERT, JEAN; COULON, AURÉLIE; DE FERAUDY, D.; ESTONBA, A.; HANKELN, THOMAS; HOCHKIRCH, AXEL; HSU, TSAI-WEN; HUANG, TSURNG-JUHN; IRIGOIEN, X.; IRIONDO, M.; KAY, KATHLEEN M.; KINITZ, TIM; KOTHERA, LINDA; LE HÉNANFF, MAXIME; LIEUTIER, F.; LOURDAIS, OLIVIER; MACRINI, CAMILA M. T.; MANZANO, C.; MARTIN, C.; MORRIS, VERONICA R. F.; NANNINGA, GERRIT; PARDO, M. A.; PLIESKE, JÖRG; POINTEAU, S.; PRESTEGAARD, TORE; QUACK, MARKUS; RICHARD, MURIELLE; SAVAGE, HARRY M.; SCHWARCZ, KAISER D.; SHADE, JESSICA; SIMMS, ELLEN L.; SOLFERINI, VERA N.; STEVENS, VIRGINIE M.; VEITH, MICHAEL; WEN, MEI-JUAN; WICKER, FLORIAN; YOST, JENNIFER M.; ZARRAONAINDIA, I.

2017-01-01

This article documents the addition of 139 microsatellite marker loci and 90 pairs of single-nucleotide polymorphism sequencing primers to the Molecular Ecology Resources Database. Loci were developed for the following species: Aglaoctenus lagotis, Costus pulverulentus, Costus scaber, Culex pipiens, Dascyllus marginatus, Lupinus nanus Benth, Phloeomyzus passerini, Podarcis muralis, Rhododendron rubropilosum Hayata var. taiwanalpinum and Zoarces viviparus. These loci were cross-tested on the following species: Culex quinquefasciatus, Rhododendron pseudochrysanthum Hay. ssp. morii (Hay.) Yamazaki and R. pseudochrysanthum Hayata. This article also documents the addition of 48 sequencing primer pairs and 90 allele-specific primers for Engraulis encrasicolus. PMID:22296658

The USDA national animal germplasm program and the aquatic species collection. In: T.R. Tiersch and C.C. Green (eds.) Cryopreservation in Aquatic Species, 2nd Edition. World Aquaculture Society, Baton Rouge, LA

USDA-ARS?s Scientific Manuscript database

Diverse genetic resources and the genetic variability within species are the raw materials by which the productivity of aquatic species populations can be increased for food production. Due to the importance of these resources there is growing international awareness that these resources are importa...

Analysis of the human diseasome using phenotype similarity between common, genetic, and infectious diseases

NASA Astrophysics Data System (ADS)

Hoehndorf, Robert; Schofield, Paul N.; Gkoutos, Georgios V.

2015-06-01

Phenotypes are the observable characteristics of an organism arising from its response to the environment. Phenotypes associated with engineered and natural genetic variation are widely recorded using phenotype ontologies in model organisms, as are signs and symptoms of human Mendelian diseases in databases such as OMIM and Orphanet. Exploiting these resources, several computational methods have been developed for integration and analysis of phenotype data to identify the genetic etiology of diseases or suggest plausible interventions. A similar resource would be highly useful not only for rare and Mendelian diseases, but also for common, complex and infectious diseases. We apply a semantic text-mining approach to identify the phenotypes (signs and symptoms) associated with over 6,000 diseases. We evaluate our text-mined phenotypes by demonstrating that they can correctly identify known disease-associated genes in mice and humans with high accuracy. Using a phenotypic similarity measure, we generate a human disease network in which diseases that have similar signs and symptoms cluster together, and we use this network to identify closely related diseases based on common etiological, anatomical as well as physiological underpinnings.

Genetics Home Reference: Boucher-Neuhäuser syndrome

MedlinePlus

... the cerebellum ). Affected individuals have an unsteady walking style (gait) and frequent falls. Another key feature of ... be inherited? More about Inheriting Genetic Conditions Diagnosis & Management Resources Genetic Testing (1 link) Genetic Testing Registry: ...

A toolkit for incorporating genetics into mainstream medical services: Learning from service development pilots in England

PubMed Central

2010-01-01

Background As advances in genetics are becoming increasingly relevant to mainstream healthcare, a major challenge is to ensure that these are integrated appropriately into mainstream medical services. In 2003, the Department of Health for England announced the availability of start-up funding for ten 'Mainstreaming Genetics' pilot services to develop models to achieve this. Methods Multiple methods were used to explore the pilots' experiences of incorporating genetics which might inform the development of new services in the future. A workshop with project staff, an email questionnaire, interviews and a thematic analysis of pilot final reports were carried out. Results Seven themes relating to the integration of genetics into mainstream medical services were identified: planning services to incorporate genetics; the involvement of genetics departments; the establishment of roles incorporating genetic activities; identifying and involving stakeholders; the challenges of working across specialty boundaries; working with multiple healthcare organisations; and the importance of cultural awareness of genetic conditions. Pilots found that the planning phase often included the need to raise awareness of genetic conditions and services and that early consideration of organisational issues such as clinic location was essential. The formal involvement of genetics departments was crucial to success; benefits included provision of clinical and educational support for staff in new roles. Recruitment and retention for new roles outside usual career pathways sometimes proved difficult. Differences in specialties' working practices and working with multiple healthcare organisations also brought challenges such as the 'genetic approach' of working with families, incompatible record systems and different approaches to health professionals' autonomous practice. 'Practice points' have been collated into a Toolkit which includes resources from the pilots, including job descriptions and clinical tools. These can be customised for reuse by other services. Conclusions Healthcare services need to translate advances in genetics into benefits for patients. Consideration of the issues presented here when incorporating genetics into mainstream medical services will help ensure that new service developments build on the body of experience gained by the pilots, to provide high quality services for patients with or at risk of genetic conditions. PMID:20470377

A toolkit for incorporating genetics into mainstream medical services: Learning from service development pilots in England.

PubMed

Bennett, Catherine L; Burke, Sarah E; Burton, Hilary; Farndon, Peter A

2010-05-14

As advances in genetics are becoming increasingly relevant to mainstream healthcare, a major challenge is to ensure that these are integrated appropriately into mainstream medical services. In 2003, the Department of Health for England announced the availability of start-up funding for ten 'Mainstreaming Genetics' pilot services to develop models to achieve this. Multiple methods were used to explore the pilots' experiences of incorporating genetics which might inform the development of new services in the future. A workshop with project staff, an email questionnaire, interviews and a thematic analysis of pilot final reports were carried out. Seven themes relating to the integration of genetics into mainstream medical services were identified: planning services to incorporate genetics; the involvement of genetics departments; the establishment of roles incorporating genetic activities; identifying and involving stakeholders; the challenges of working across specialty boundaries; working with multiple healthcare organisations; and the importance of cultural awareness of genetic conditions. Pilots found that the planning phase often included the need to raise awareness of genetic conditions and services and that early consideration of organisational issues such as clinic location was essential. The formal involvement of genetics departments was crucial to success; benefits included provision of clinical and educational support for staff in new roles. Recruitment and retention for new roles outside usual career pathways sometimes proved difficult. Differences in specialties' working practices and working with multiple healthcare organisations also brought challenges such as the 'genetic approach' of working with families, incompatible record systems and different approaches to health professionals' autonomous practice. 'Practice points' have been collated into a Toolkit which includes resources from the pilots, including job descriptions and clinical tools. These can be customised for reuse by other services. Healthcare services need to translate advances in genetics into benefits for patients. Consideration of the issues presented here when incorporating genetics into mainstream medical services will help ensure that new service developments build on the body of experience gained by the pilots, to provide high quality services for patients with or at risk of genetic conditions.

[Book review] Fish Gene Pools: preservation of genetic resources in relation to wild fish stocks, edited by N. Ryman

USGS Publications Warehouse

Simon, R.C.

1984-01-01

Review of: Fish Gene Pools: Preservation of Genetic Resources in Relation to Wild Fish Stocks. Edited by N. Ryman. The Editorial Service/FRN, Box 6710, S-11385, Stockholm, Sweden. 1981. 111 pages. $16.00 (paper).

Maize Genetic Resources Collections – Utilizing a Treasure Trove

USDA-ARS?s Scientific Manuscript database

The maize genetic resource collection managed by the USDA-ARS's National Plant Germplasm System is heavily utilized by researchers and educators. A collection of landraces, inbred lines from public and private sector sources, synthetics and key populations, it serves both as a living snapshot of th...

National Plant Germplasm System: Critical Role of Customer Service

USDA-ARS?s Scientific Manuscript database

The National Plant Germplasm System (NPGS) conserves plant genetic resources, not only for use by future generations, but for immediate use by scientists and educators around the world. With a great deal of interaction between genebank curators and users of plant genetic resources, customer service...

Mining natural variation for maize improvement: Selection on phenotypes and genes

USDA-ARS?s Scientific Manuscript database

Maize is highly genetically and phenotypically diverse. Tropical maize and teosinte are important genetic resources that harbor unique alleles not found in temperate maize hybrids. To access these resources, breeders must be able to extract favorable unique alleles from tropical maize and teosinte f...

International efforts to protect the global cotton genetic resources

USDA-ARS?s Scientific Manuscript database

The genetic resources of cotton are classified into five tetraploid species in the primary gene pool, 20 diploid species in the secondary gene pool, and 25 diploid species in the tertiary gene pool. Unlike several globally important grain crops, the Consultative Group on International Agricultural R...

Beyond botany to genetic resource preservation: the S. P. Vander Kloet Vaccinium L. collections

USDA-ARS?s Scientific Manuscript database

Dr. S. P. Vander Kloet, botanist, traveled the world examining and obtaining specimens to redefine infrageneric taxonomic units within Vaccinium L., family Ericaceae. Besides his botanical treatises, his legacy includes herbarium voucher specimens and ex situ genetic resource collections including a...

Genetic Resources in the “Calabaza Pipiana” Squash (Cucurbita argyrosperma) in Mexico: Genetic Diversity, Genetic Differentiation and Distribution Models

PubMed Central

Sánchez-de la Vega, Guillermo; Castellanos-Morales, Gabriela; Gámez, Niza; Hernández-Rosales, Helena S.; Vázquez-Lobo, Alejandra; Aguirre-Planter, Erika; Jaramillo-Correa, Juan P.; Montes-Hernández, Salvador; Lira-Saade, Rafael; Eguiarte, Luis E.

2018-01-01

Analyses of genetic variation allow understanding the origin, diversification and genetic resources of cultivated plants. Domesticated taxa and their wild relatives are ideal systems for studying genetic processes of plant domestication and their joint is important to evaluate the distribution of their genetic resources. Such is the case of the domesticated subspecies C. argyrosperma ssp. argyrosperma, known in Mexico as calabaza pipiana, and its wild relative C. argyrosperma ssp. sororia. The main aim of this study was to use molecular data (microsatellites) to assess the levels of genetic variation and genetic differentiation within and among populations of domesticated argyrosperma across its distribution in Mexico in comparison to its wild relative, sororia, and to identify environmental suitability in previously proposed centers of domestication. We analyzed nine unlinked nuclear microsatellite loci to assess levels of diversity and distribution of genetic variation within and among populations in 440 individuals from 19 populations of cultivated landraces of argyrosperma and from six wild populations of sororia, in order to conduct a first systematic analysis of their genetic resources. We also used species distribution models (SDMs) for sororia to identify changes in this wild subspecies’ distribution from the Holocene (∼6,000 years ago) to the present, and to assess the presence of suitable environmental conditions in previously proposed domestication sites. Genetic variation was similar among subspecies (HE = 0.428 in sororia, and HE = 0.410 in argyrosperma). Nine argyrosperma populations showed significant levels of inbreeding. Both subspecies are well differentiated, and genetic differentiation (FST) among populations within each subspecies ranged from 0.152 to 0.652. Within argyrosperma we found three genetic groups (Northern Mexico, Yucatan Peninsula, including Michoacan and Veracruz, and Pacific coast plus Durango). We detected low levels of gene flow among populations at a regional scale (<0.01), except for the Yucatan Peninsula, and the northern portion of the Pacific Coast. Our analyses suggested that the Isthmus of Tehuantepec is an effective barrier isolating southern populations. Our SDM results indicate that environmental characteristics in the Balsas-Jalisco region, a potential center of domestication, were suitable for the presence of sororia during the Holocene. PMID:29662500

Genetic Resources in the "Calabaza Pipiana" Squash (Cucurbita argyrosperma) in Mexico: Genetic Diversity, Genetic Differentiation and Distribution Models.

PubMed

Sánchez-de la Vega, Guillermo; Castellanos-Morales, Gabriela; Gámez, Niza; Hernández-Rosales, Helena S; Vázquez-Lobo, Alejandra; Aguirre-Planter, Erika; Jaramillo-Correa, Juan P; Montes-Hernández, Salvador; Lira-Saade, Rafael; Eguiarte, Luis E

2018-01-01

Analyses of genetic variation allow understanding the origin, diversification and genetic resources of cultivated plants. Domesticated taxa and their wild relatives are ideal systems for studying genetic processes of plant domestication and their joint is important to evaluate the distribution of their genetic resources. Such is the case of the domesticated subspecies C. argyrosperma ssp. argyrosperma , known in Mexico as calabaza pipiana , and its wild relative C. argyrosperma ssp. sororia . The main aim of this study was to use molecular data (microsatellites) to assess the levels of genetic variation and genetic differentiation within and among populations of domesticated argyrosperma across its distribution in Mexico in comparison to its wild relative, sororia , and to identify environmental suitability in previously proposed centers of domestication. We analyzed nine unlinked nuclear microsatellite loci to assess levels of diversity and distribution of genetic variation within and among populations in 440 individuals from 19 populations of cultivated landraces of argyrosperma and from six wild populations of sororia , in order to conduct a first systematic analysis of their genetic resources. We also used species distribution models (SDMs) for sororia to identify changes in this wild subspecies' distribution from the Holocene (∼6,000 years ago) to the present, and to assess the presence of suitable environmental conditions in previously proposed domestication sites. Genetic variation was similar among subspecies ( H E = 0.428 in sororia , and H E = 0.410 in argyrosperma ). Nine argyrosperma populations showed significant levels of inbreeding. Both subspecies are well differentiated, and genetic differentiation ( F ST ) among populations within each subspecies ranged from 0.152 to 0.652. Within argyrosperma we found three genetic groups (Northern Mexico, Yucatan Peninsula, including Michoacan and Veracruz, and Pacific coast plus Durango). We detected low levels of gene flow among populations at a regional scale (<0.01), except for the Yucatan Peninsula, and the northern portion of the Pacific Coast. Our analyses suggested that the Isthmus of Tehuantepec is an effective barrier isolating southern populations. Our SDM results indicate that environmental characteristics in the Balsas-Jalisco region, a potential center of domestication, were suitable for the presence of sororia during the Holocene.

PatGen--a consolidated resource for searching genetic patent sequences.

PubMed

Rouse, Richard J D; Castagnetto, Jesus; Niedner, Roland H

2005-04-15

Compared to the wealth of online resources covering genomic, proteomic and derived data the Bioinformatics community is rather underserved when it comes to patent information related to biological sequences. The current online resources are either incomplete or rather expensive. This paper describes, PatGen, an integrated database containing data from bioinformatic and patent resources. This effort addresses the inconsistency of publicly available genetic patent data coverage by providing access to a consolidated dataset. PatGen can be searched at http://www.patgendb.com rjdrouse@patentinformatics.com.

Factors influencing organizational adoption and implementation of clinical genetic services.

PubMed

Hamilton, Alison B; Oishi, Sabine; Yano, Elizabeth M; Gammage, Cynthia E; Marshall, Nell J; Scheuner, Maren T

2014-03-01

We sought to identify characteristics of genetic services that facilitate or hinder adoption. We conducted semi-structured key informant interviews in five clinical specialties (primary care, medical oncology, neurology, cardiology, pathology/laboratory medicine) within 13 Veterans Administration facilities. Genetic services (defined as genetic testing and consultation) were not typically characterized by informants (n = 64) as advantageous for their facilities or their patients; compatible with organizational norms of low cost and high clinical impact; or applicable to patient populations or norms of clinical care. Furthermore, genetic services had not been systematically adopted in most facilities because of their complexity: knowledge of and expertise on genetic testing was limited, and organizational barriers to utilization of genetic services were formidable. The few facilities that had some success with implementation of genetic services had knowledgeable clinicians interested in developing services and organizational-level facilitators such as accessible genetic test-ordering processes. Adoption and implementation of genetic services will require a multilevel effort that includes education of providers and administrators, opportunities for observing the benefits of genetic medicine, strategies for reducing the complexity of genomic medicine, expanded strategies for accessing genetics expertise and streamlining utilization, and resources dedicated to assessing the value of genetic information for the outcomes that matter to health-care organizations.

The U.S. Culture Collection Network Responding to the Requirements of the Nagoya Protocol on Access and Benefit Sharing

PubMed Central

Barker, Katharine B.; Barton, Hazel A.; Boundy-Mills, Kyria; Brown, Daniel R.; Coddington, Jonathan A.; Cook, Kevin; Desmeth, Philippe; Geiser, David; Glaeser, Jessie A.; Greene, Stephanie; Kang, Seogchan; Lomas, Michael W.; Melcher, Ulrich; Miller, Scott E.; Nobles, David R.; Owens, Kristina J.; Reichman, Jerome H.; da Silva, Manuela; Wertz, John; Whitworth, Cale; Smith, David

2017-01-01

ABSTRACT The U.S. Culture Collection Network held a meeting to share information about how culture collections are responding to the requirements of the recently enacted Nagoya Protocol on Access to Genetic Resources and the Fair and Equitable Sharing of Benefits Arising from their Utilization to the Convention on Biological Diversity (CBD). The meeting included representatives of many culture collections and other biological collections, the U.S. Department of State, U.S. Department of Agriculture, Secretariat of the CBD, interested scientific societies, and collection groups, including Scientific Collections International and the Global Genome Biodiversity Network. The participants learned about the policies of the United States and other countries regarding access to genetic resources, the definition of genetic resources, and the status of historical materials and genetic sequence information. Key topics included what constitutes access and how the CBD Access and Benefit-Sharing Clearing-House can help guide researchers through the process of obtaining Prior Informed Consent on Mutually Agreed Terms. U.S. scientists and their international collaborators are required to follow the regulations of other countries when working with microbes originally isolated outside the United States, and the local regulations required by the Nagoya Protocol vary by the country of origin of the genetic resource. Managers of diverse living collections in the United States described their holdings and their efforts to provide access to genetic resources. This meeting laid the foundation for cooperation in establishing a set of standard operating procedures for U.S. and international culture collections in response to the Nagoya Protocol. PMID:28811341

The U.S. Culture Collection Network Responding to the Requirements of the Nagoya Protocol on Access and Benefit Sharing.

PubMed

McCluskey, Kevin; Barker, Katharine B; Barton, Hazel A; Boundy-Mills, Kyria; Brown, Daniel R; Coddington, Jonathan A; Cook, Kevin; Desmeth, Philippe; Geiser, David; Glaeser, Jessie A; Greene, Stephanie; Kang, Seogchan; Lomas, Michael W; Melcher, Ulrich; Miller, Scott E; Nobles, David R; Owens, Kristina J; Reichman, Jerome H; da Silva, Manuela; Wertz, John; Whitworth, Cale; Smith, David

2017-08-15

The U.S. Culture Collection Network held a meeting to share information about how culture collections are responding to the requirements of the recently enacted Nagoya Protocol on Access to Genetic Resources and the Fair and Equitable Sharing of Benefits Arising from their Utilization to the Convention on Biological Diversity (CBD). The meeting included representatives of many culture collections and other biological collections, the U.S. Department of State, U.S. Department of Agriculture, Secretariat of the CBD, interested scientific societies, and collection groups, including Scientific Collections International and the Global Genome Biodiversity Network. The participants learned about the policies of the United States and other countries regarding access to genetic resources, the definition of genetic resources, and the status of historical materials and genetic sequence information. Key topics included what constitutes access and how the CBD Access and Benefit-Sharing Clearing-House can help guide researchers through the process of obtaining Prior Informed Consent on Mutually Agreed Terms. U.S. scientists and their international collaborators are required to follow the regulations of other countries when working with microbes originally isolated outside the United States, and the local regulations required by the Nagoya Protocol vary by the country of origin of the genetic resource. Managers of diverse living collections in the United States described their holdings and their efforts to provide access to genetic resources. This meeting laid the foundation for cooperation in establishing a set of standard operating procedures for U.S. and international culture collections in response to the Nagoya Protocol.

Phylogenetic analysis of Tibetan mastiffs based on mitochondrial hypervariable region I.

PubMed

Ren, Zhanjun; Chen, Huiling; Yang, Xuejiao; Zhang, Chengdong

2017-03-01

Recently, the number of Tibetan mastiffs, which is a precious germplasm resource and cultural heritage, is decreasing sharply. Therefore, the genetic diversity of Tibetan mastiffs needs to be studied to clarify its phylogenetics relationships and lay the foundation for resource protection, rational development and utilization of Tibetan mastiffs. We sequenced hypervariable region I of mitochondrial DNA (mtDNA) of 110 individuals from Tibet region and Gansu province. A total of 12 polymorphic sites were identified which defined eight haplotypes of which H4 and H8 were unique to Tibetan population with H8 being identified first. The haplotype diversity (Hd: 0.808), nucleotide diversity (Pi: 0.603%), the average number of nucleotide difference (K: 3.917) of Tibetan mastiffs from Gansu were higher than those from Tibet region (Hd: 0.794; Pi: 0.589%; K: 3.831), which revealed higher genetic diversity in Gansu. In terms of total population, the genetic variation was low. The median-joining network and phylogenetic tree based on the mtDNA hypervariable region I showed that Tibetan mastiffs originated from grey wolves, as the other domestic dogs and had different history of maternal origin. The mismatch distribution analysis and neutrality tests indicated that Tibetan mastiffs were in genetic equilibrium or in a population decline.

Genetic Diversity of Cowpea (Vigna unguiculata (L.) Walp.) Accession in Kenya Gene Bank Based on Simple Sequence Repeat Markers.

PubMed

Wamalwa, Emily N; Muoma, John; Wekesa, Clabe

2016-01-01

Increased agricultural production is an urgent issue. Projected global population is 9 million people by mid of this century. Estimation projects death of 1 million people for lack of food quality (micronutrient deficit) and quantity (protein deficit). Majority of these people will be living in developing countries. Other global challenges include shrinking cultivable lands, salinity, and flooding due to climate changes, new emerging pathogens, and pests. These affect crop production. Furthermore, they are major threats to crop genetic resources and food security. Genetic diversity in cultivated crops indicates gene pool richness. It is the greatest resource for plant breeders to select lines that enhance food security. This study was conducted by Masinde Muliro University to evaluate genetic diversity in 19 cowpea accessions from Kenya national gene bank. Accessions clustered into two major groups. High divergence was observed between accessions from Ethiopia and Australia and those from Western Kenya. Upper Volta accessions were closely related to those from Western Kenya. Low variation was observed between accessions from Eastern and Rift Valley than those from Western and Coastal regions of Kenya. Diversity obtained in this study can further be exploited for the improvement of cowpea in Kenya as a measure of food security.

COTIP: Cotton TILLING Platform, a Resource for Plant Improvement and Reverse Genetic Studies

PubMed Central

Aslam, Usman; Cheema, Hafiza M. N.; Ahmad, Sheraz; Khan, Iqrar A.; Malik, Waqas; Khan, Asif A.

2016-01-01

Cotton is cultivated worldwide for its white fiber, of which around 90% is tetraploid upland cotton (Gossypium hirsutum L.) carrying both A and D genome. Since centuries, yield increasing efforts for the cotton crop by conventional breeding approaches have caused an extensive erosion of natural genetic variability. Mutation based improvement strategies provide an effective way of creating new allelic variations. Targeting Induced Local Lesions IN Genomes (TILLING) provides a mutation based reverse genetic strategy to create and evaluate induced genetic variability at DNA level. Here, we report development and testing of TILLING populations of allotetraploid cotton (G. hirsutum) for functional genomic studies and mutation based enrichment of cotton genetic resources. Seed of two cotton cultivars “PB-899 and PB-900” were mutagenized with 0.3 and 0.2% (v/v) ethyl methanesulfonate, respectively. The phenotyping of M1 and M2 populations presented numerous mutants regarding the branching pattern, leaf morphology, disease resistance, photosynthetic lesions and flower sterility. Molecular screening for point mutations was performed by TILLING PCR aided CEL1 mismatch cleavage. To estimate the mutation frequency in the mutant genomes, five gene classes were TILLed in 8000 M2 plants of each var. “PB-899” and “PB-900.” These include actin (GhACT), Pectin Methyl Esterase (GhPME), sucrose synthase (GhSUS), resistance gene analog, and defense response gene (DRGs). The var. PB-899 was harboring 47% higher mutation induction rate than PB-900. The highest rate of mutation frequency was identified for NAC-TF5 (EU706348) of DRGs class, ranging from 1/58 kb in PB-899 to 1/105 kb in PB-900. The mutation screening assay revealed the presence of significant proportion of induced mutations in cotton TILLING populations such as 1/153 kb and 1/326 kb in var. “PB-899” and “PB-900,” respectively. The establishment of a cotton TILLING platform (COTIP) and data obtained from the resource TILLING population suggest its effectiveness in widening the genetic bases of cotton for improvement and utilizing it for subsequent reverse genetic studies of various genes. PMID:28082993

Assessing and Exploiting Functional Diversity in Germplasm Pools to Enhance Abiotic Stress Adaptation and Yield in Cereals and Food Legumes

PubMed Central

Dwivedi, Sangam L.; Scheben, Armin; Edwards, David; Spillane, Charles; Ortiz, Rodomiro

2017-01-01

There is a need to accelerate crop improvement by introducing alleles conferring host plant resistance, abiotic stress adaptation, and high yield potential. Elite cultivars, landraces and wild relatives harbor useful genetic variation that needs to be more easily utilized in plant breeding. We review genome-wide approaches for assessing and identifying alleles associated with desirable agronomic traits in diverse germplasm pools of cereals and legumes. Major quantitative trait loci and single nucleotide polymorphisms (SNPs) associated with desirable agronomic traits have been deployed to enhance crop productivity and resilience. These include alleles associated with variation conferring enhanced photoperiod and flowering traits. Genetic variants in the florigen pathway can provide both environmental flexibility and improved yields. SNPs associated with length of growing season and tolerance to abiotic stresses (precipitation, high temperature) are valuable resources for accelerating breeding for drought-prone environments. Both genomic selection and genome editing can also harness allelic diversity and increase productivity by improving multiple traits, including phenology, plant architecture, yield potential and adaptation to abiotic stresses. Discovering rare alleles and useful haplotypes also provides opportunities to enhance abiotic stress adaptation, while epigenetic variation has potential to enhance abiotic stress adaptation and productivity in crops. By reviewing current knowledge on specific traits and their genetic basis, we highlight recent developments in the understanding of crop functional diversity and identify potential candidate genes for future use. The storage and integration of genetic, genomic and phenotypic information will play an important role in ensuring broad and rapid application of novel genetic discoveries by the plant breeding community. Exploiting alleles for yield-related traits would allow improvement of selection efficiency and overall genetic gain of multigenic traits. An integrated approach involving multiple stakeholders specializing in management and utilization of genetic resources, crop breeding, molecular biology and genomics, agronomy, stress tolerance, and reproductive/seed biology will help to address the global challenge of ensuring food security in the face of growing resource demands and climate change induced stresses. PMID:28900432

Assessing and Exploiting Functional Diversity in Germplasm Pools to Enhance Abiotic Stress Adaptation and Yield in Cereals and Food Legumes.

PubMed

Dwivedi, Sangam L; Scheben, Armin; Edwards, David; Spillane, Charles; Ortiz, Rodomiro

2017-01-01

There is a need to accelerate crop improvement by introducing alleles conferring host plant resistance, abiotic stress adaptation, and high yield potential. Elite cultivars, landraces and wild relatives harbor useful genetic variation that needs to be more easily utilized in plant breeding. We review genome-wide approaches for assessing and identifying alleles associated with desirable agronomic traits in diverse germplasm pools of cereals and legumes. Major quantitative trait loci and single nucleotide polymorphisms (SNPs) associated with desirable agronomic traits have been deployed to enhance crop productivity and resilience. These include alleles associated with variation conferring enhanced photoperiod and flowering traits. Genetic variants in the florigen pathway can provide both environmental flexibility and improved yields. SNPs associated with length of growing season and tolerance to abiotic stresses (precipitation, high temperature) are valuable resources for accelerating breeding for drought-prone environments. Both genomic selection and genome editing can also harness allelic diversity and increase productivity by improving multiple traits, including phenology, plant architecture, yield potential and adaptation to abiotic stresses. Discovering rare alleles and useful haplotypes also provides opportunities to enhance abiotic stress adaptation, while epigenetic variation has potential to enhance abiotic stress adaptation and productivity in crops. By reviewing current knowledge on specific traits and their genetic basis, we highlight recent developments in the understanding of crop functional diversity and identify potential candidate genes for future use. The storage and integration of genetic, genomic and phenotypic information will play an important role in ensuring broad and rapid application of novel genetic discoveries by the plant breeding community. Exploiting alleles for yield-related traits would allow improvement of selection efficiency and overall genetic gain of multigenic traits. An integrated approach involving multiple stakeholders specializing in management and utilization of genetic resources, crop breeding, molecular biology and genomics, agronomy, stress tolerance, and reproductive/seed biology will help to address the global challenge of ensuring food security in the face of growing resource demands and climate change induced stresses.

Investigation on Reservoir Operation of Agricultural Water Resources Management for Drought Mitigation

NASA Astrophysics Data System (ADS)

Cheng, C. L.

2015-12-01

Investigation on Reservoir Operation of Agricultural Water Resources Management for Drought Mitigation Chung-Lien Cheng, Wen-Ping Tsai, Fi-John Chang* Department of Bioenvironmental Systems Engineering, National Taiwan University, Da-An District, Taipei 10617, Taiwan, ROC.Corresponding author: Fi-John Chang (changfj@ntu.edu.tw) AbstractIn Taiwan, the population growth and economic development has led to considerable and increasing demands for natural water resources in the last decades. Under such condition, water shortage problems have frequently occurred in northern Taiwan in recent years such that water is usually transferred from irrigation sectors to public sectors during drought periods. Facing the uneven spatial and temporal distribution of water resources and the problems of increasing water shortages, it is a primary and critical issue to simultaneously satisfy multiple water uses through adequate reservoir operations for sustainable water resources management. Therefore, we intend to build an intelligent reservoir operation system for the assessment of agricultural water resources management strategy in response to food security during drought periods. This study first uses the grey system to forecast the agricultural water demand during February and April for assessing future agricultural water demands. In the second part, we build an intelligent water resources system by using the non-dominated sorting genetic algorithm-II (NSGA-II), an optimization tool, for searching the water allocation series based on different water demand scenarios created from the first part to optimize the water supply operation for different water sectors. The results can be a reference guide for adequate agricultural water resources management during drought periods. Keywords: Non-dominated sorting genetic algorithm-II (NSGA-II); Grey System; Optimization; Agricultural Water Resources Management.

Dynamics of list-server discussion on genetically modified foods.

PubMed

Triunfol, Marcia L; Hines, Pamela J

2004-04-01

Computer-mediated discussion lists, or list-servers, are popular tools in settings ranging from professional to personal to educational. A discussion list on genetically modified food (GMF) was created in September 2000 as part of the Forum on Genetically Modified Food developed by Science Controversies: Online Partnerships in Education (SCOPE), an educational project that uses computer resources to aid research and learning around unresolved scientific questions. The discussion list "GMF-Science" was actively supported from January 2001 to May 2002. The GMF-Science list welcomed anyone interested in discussing the controversies surrounding GMF. Here, we analyze the dynamics of the discussions and how the GMF-Science list may contribute to learning. Activity on the GMF-Science discussion list reflected some but not all the controversies that were appearing in more traditional publication formats, broached other topics not well represented in the published literature, and tended to leave undiscussed the more technical research developments.

A Simple Sequence Repeat- and Single-Nucleotide Polymorphism-Based Genetic Linkage Map of the Brown Planthopper, Nilaparvata lugens

PubMed Central

Jairin, Jirapong; Kobayashi, Tetsuya; Yamagata, Yoshiyuki; Sanada-Morimura, Sachiyo; Mori, Kazuki; Tashiro, Kosuke; Kuhara, Satoru; Kuwazaki, Seigo; Urio, Masahiro; Suetsugu, Yoshitaka; Yamamoto, Kimiko; Matsumura, Masaya; Yasui, Hideshi

2013-01-01

In this study, we developed the first genetic linkage map for the major rice insect pest, the brown planthopper (BPH, Nilaparvata lugens). The linkage map was constructed by integrating linkage data from two backcross populations derived from three inbred BPH strains. The consensus map consists of 474 simple sequence repeats, 43 single-nucleotide polymorphisms, and 1 sequence-tagged site, for a total of 518 markers at 472 unique positions in 17 linkage groups. The linkage groups cover 1093.9 cM, with an average distance of 2.3 cM between loci. The average number of marker loci per linkage group was 27.8. The sex-linkage group was identified by exploiting X-linked and Y-specific markers. Our linkage map and the newly developed markers used to create it constitute an essential resource and a useful framework for future genetic analyses in BPH. PMID:23204257

Establishing sugarcane (Saccharum spp.) genetic resources for in vitro storage and cryopreservation

USDA-ARS?s Scientific Manuscript database

Sugarcane (Saccharum spp.) is used to produce sugar, a variety of alcoholic beverages, bagasse and industrial ethanol utilized in making fuel. In production fields, sugarcane is propagated vegetatively and currently, the crop’s genetic resources are also preserved as field plantings. The National Pl...

Molecular fingerprinting of cacao (Theobroma cacao L.) genetic resources in the Dominican Republic

USDA-ARS?s Scientific Manuscript database

Cacao (Theobroma cacao L.) is a significant agricultural commodity in the Dominican Republic ranking 11th in the world and number one in organic cacao exports. Dominican cacao genetic resources are maintained, propagated and distributed nationally out of the IDIAF’s Mata Larga research stations. T...

Important Hawaiian tree species in need of genetic conservation

Treesearch

Robert D. Hauff

2017-01-01

Resource managers in Hawaii face unique forest conservation challenges. Invasive species continue to inundate the remote island archipelago, directly threatening its forest resources. Hawaii has the largest number (> 400) of endangered plants in the United States, and managers use genetic approaches to preserve these small populations which are often island...

Pharmacogenomics to Revive Drug Development in Cardiovascular Disease.

PubMed

Dubé, Marie-Pierre; de Denus, Simon; Tardif, Jean-Claude

2016-02-01

Investment in cardiovascular drug development is on the decline as large cardiovascular outcomes trials require considerable investments in time, efforts and financial resources. Pharmacogenomics has the potential to help revive the cardiovascular drug development pipeline by providing new and better drug targets at an earlier stage and by enabling more efficient outcomes trials. This article will review some of the recent developments highlighting the value of pharmacogenomics for drug development. We discuss how genetic biomarkers can enable the conduct of more efficient clinical outcomes trials by enriching patient populations for good responders to the medication. In addition, we assess past drug development programs which support the added value of selecting drug targets that have established genetic evidence supporting the targeted mechanism of disease. Finally, we discuss how pharmacogenomics can provide valuable evidence linking a drug target to clinically relevant outcomes, enabling novel drug discovery and drug repositioning opportunities.

Recommendations for Genetic Variation Data Capture in Developing Countries to Ensure a Comprehensive Worldwide Data Collection

PubMed Central

Patrinos, George P; Al Aama, Jumana; Al Aqeel, Aida; Al-Mulla, Fahd; Borg, Joseph; Devereux, Andrew; Felice, Alex E; Macrae, Finlay; Marafie, Makia J; Petersen, Michael B; Qi, Ming; Ramesar, Rajkumar S; Zlotogora, Joel; Cotton, Richard GH

2011-01-01

Developing countries have significantly contributed to the elucidation of the genetic basis of both common and rare disorders, providing an invaluable resource of cases due to large family sizes, consanguinity, and potential founder effects. Moreover, the recognized depth of genomic variation in indigenous African populations, reflecting the ancient origins of humanity on the African continent, and the effect of selection pressures on the genome, will be valuable in understanding the range of both pathological and nonpathological variations. The involvement of these populations in accurately documenting the extant genetic heterogeneity is more than essential. Developing nations are regarded as key contributors to the Human Variome Project (HVP; http://www.humanvariomeproject.org), a major effort to systematically collect mutations that contribute to or cause human disease and create a cyber infrastructure to tie databases together. However, biomedical research has not been the primary focus in these countries even though such activities are likely to produce economic and health benefits for all. Here, we propose several recommendations and guidelines to facilitate participation of developing countries in genetic variation data documentation, ensuring an accurate and comprehensive worldwide data collection. We also summarize a few well-coordinated genetic data collection initiatives that would serve as paradigms for similar projects. Hum Mutat 31:1–8, 2010. © 2010 Wiley-Liss, Inc. PMID:21089065

Mouse Models for Drug Discovery. Can New Tools and Technology Improve Translational Power?

PubMed Central

Zuberi, Aamir; Lutz, Cathleen

2016-01-01

Abstract The use of mouse models in biomedical research and preclinical drug evaluation is on the rise. The advent of new molecular genome-altering technologies such as CRISPR/Cas9 allows for genetic mutations to be introduced into the germ line of a mouse faster and less expensively than previous methods. In addition, the rapid progress in the development and use of somatic transgenesis using viral vectors, as well as manipulations of gene expression with siRNAs and antisense oligonucleotides, allow for even greater exploration into genomics and systems biology. These technological advances come at a time when cost reductions in genome sequencing have led to the identification of pathogenic mutations in patient populations, providing unprecedented opportunities in the use of mice to model human disease. The ease of genetic engineering in mice also offers a potential paradigm shift in resource sharing and the speed by which models are made available in the public domain. Predictively, the knowledge alone that a model can be quickly remade will provide relief to resources encumbered by licensing and Material Transfer Agreements. For decades, mouse strains have provided an exquisite experimental tool to study the pathophysiology of the disease and assess therapeutic options in a genetically defined system. However, a major limitation of the mouse has been the limited genetic diversity associated with common laboratory mice. This has been overcome with the recent development of the Collaborative Cross and Diversity Outbred mice. These strains provide new tools capable of replicating genetic diversity to that approaching the diversity found in human populations. The Collaborative Cross and Diversity Outbred strains thus provide a means to observe and characterize toxicity or efficacy of new therapeutic drugs for a given population. The combination of traditional and contemporary mouse genome editing tools, along with the addition of genetic diversity in new modeling systems, are synergistic and serve to make the mouse a better model for biomedical research, enhancing the potential for preclinical drug discovery and personalized medicine. PMID:28053071

Achievements and prospects of genomics-assisted breeding in three legume crops of the semi-arid tropics.

PubMed

Varshney, Rajeev K; Mohan, S Murali; Gaur, Pooran M; Gangarao, N V P R; Pandey, Manish K; Bohra, Abhishek; Sawargaonkar, Shrikant L; Chitikineni, Annapurna; Kimurto, Paul K; Janila, Pasupuleti; Saxena, K B; Fikre, Asnake; Sharma, Mamta; Rathore, Abhishek; Pratap, Aditya; Tripathi, Shailesh; Datta, Subhojit; Chaturvedi, S K; Mallikarjuna, Nalini; Anuradha, G; Babbar, Anita; Choudhary, Arbind K; Mhase, M B; Bharadwaj, Ch; Mannur, D M; Harer, P N; Guo, Baozhu; Liang, Xuanqiang; Nadarajan, N; Gowda, C L L

2013-12-01

Advances in next-generation sequencing and genotyping technologies have enabled generation of large-scale genomic resources such as molecular markers, transcript reads and BAC-end sequences (BESs) in chickpea, pigeonpea and groundnut, three major legume crops of the semi-arid tropics. Comprehensive transcriptome assemblies and genome sequences have either been developed or underway in these crops. Based on these resources, dense genetic maps, QTL maps as well as physical maps for these legume species have also been developed. As a result, these crops have graduated from 'orphan' or 'less-studied' crops to 'genomic resources rich' crops. This article summarizes the above-mentioned advances in genomics and genomics-assisted breeding applications in the form of marker-assisted selection (MAS) for hybrid purity assessment in pigeonpea; marker-assisted backcrossing (MABC) for introgressing QTL region for drought-tolerance related traits, Fusarium wilt (FW) resistance and Ascochyta blight (AB) resistance in chickpea; late leaf spot (LLS), leaf rust and nematode resistance in groundnut. We critically present the case of use of other modern breeding approaches like marker-assisted recurrent selection (MARS) and genomic selection (GS) to utilize the full potential of genomics-assisted breeding for developing superior cultivars with enhanced tolerance to various environmental stresses. In addition, this article recommends the use of advanced-backcross (AB-backcross) breeding and development of specialized populations such as multi-parents advanced generation intercross (MAGIC) for creating new variations that will help in developing superior lines with broadened genetic base. In summary, we propose the use of integrated genomics and breeding approach in these legume crops to enhance crop productivity in marginal environments ensuring food security in developing countries. Copyright © 2012 Elsevier Inc. All rights reserved.

The Transgenic RNAi Project at Harvard Medical School: Resources and Validation.

PubMed

Perkins, Lizabeth A; Holderbaum, Laura; Tao, Rong; Hu, Yanhui; Sopko, Richelle; McCall, Kim; Yang-Zhou, Donghui; Flockhart, Ian; Binari, Richard; Shim, Hye-Seok; Miller, Audrey; Housden, Amy; Foos, Marianna; Randkelv, Sakara; Kelley, Colleen; Namgyal, Pema; Villalta, Christians; Liu, Lu-Ping; Jiang, Xia; Huan-Huan, Qiao; Wang, Xia; Fujiyama, Asao; Toyoda, Atsushi; Ayers, Kathleen; Blum, Allison; Czech, Benjamin; Neumuller, Ralph; Yan, Dong; Cavallaro, Amanda; Hibbard, Karen; Hall, Don; Cooley, Lynn; Hannon, Gregory J; Lehmann, Ruth; Parks, Annette; Mohr, Stephanie E; Ueda, Ryu; Kondo, Shu; Ni, Jian-Quan; Perrimon, Norbert

2015-11-01

To facilitate large-scale functional studies in Drosophila, the Drosophila Transgenic RNAi Project (TRiP) at Harvard Medical School (HMS) was established along with several goals: developing efficient vectors for RNAi that work in all tissues, generating a genome-scale collection of RNAi stocks with input from the community, distributing the lines as they are generated through existing stock centers, validating as many lines as possible using RT-qPCR and phenotypic analyses, and developing tools and web resources for identifying RNAi lines and retrieving existing information on their quality. With these goals in mind, here we describe in detail the various tools we developed and the status of the collection, which is currently composed of 11,491 lines and covering 71% of Drosophila genes. Data on the characterization of the lines either by RT-qPCR or phenotype is available on a dedicated website, the RNAi Stock Validation and Phenotypes Project (RSVP, http://www.flyrnai.org/RSVP.html), and stocks are available from three stock centers, the Bloomington Drosophila Stock Center (United States), National Institute of Genetics (Japan), and TsingHua Fly Center (China). Copyright © 2015 by the Genetics Society of America.

ExPASy: SIB bioinformatics resource portal.

PubMed

Artimo, Panu; Jonnalagedda, Manohar; Arnold, Konstantin; Baratin, Delphine; Csardi, Gabor; de Castro, Edouard; Duvaud, Séverine; Flegel, Volker; Fortier, Arnaud; Gasteiger, Elisabeth; Grosdidier, Aurélien; Hernandez, Céline; Ioannidis, Vassilios; Kuznetsov, Dmitry; Liechti, Robin; Moretti, Sébastien; Mostaguir, Khaled; Redaschi, Nicole; Rossier, Grégoire; Xenarios, Ioannis; Stockinger, Heinz

2012-07-01

ExPASy (http://www.expasy.org) has worldwide reputation as one of the main bioinformatics resources for proteomics. It has now evolved, becoming an extensible and integrative portal accessing many scientific resources, databases and software tools in different areas of life sciences. Scientists can henceforth access seamlessly a wide range of resources in many different domains, such as proteomics, genomics, phylogeny/evolution, systems biology, population genetics, transcriptomics, etc. The individual resources (databases, web-based and downloadable software tools) are hosted in a 'decentralized' way by different groups of the SIB Swiss Institute of Bioinformatics and partner institutions. Specifically, a single web portal provides a common entry point to a wide range of resources developed and operated by different SIB groups and external institutions. The portal features a search function across 'selected' resources. Additionally, the availability and usage of resources are monitored. The portal is aimed for both expert users and people who are not familiar with a specific domain in life sciences. The new web interface provides, in particular, visual guidance for newcomers to ExPASy.

FORT Molecular Ecology Laboratory

USGS Publications Warehouse

Oyler-McCance, Sara J.; Stevens, P.D.

2011-01-01

The mission of the U.S. Geological Survey (USGS) at the Fort Collins Science Center Molecular Ecology Laboratory is to use the tools and concepts of molecular genetics to address a variety of complex management questions and conservation issues facing the management of the Nation's fish and wildlife resources. Together with our partners, we design and implement studies to document genetic diversity and the distribution of genetic variation among individuals, populations, and species. Information from these studies is used to support wildlife-management planning and conservation actions. Current and past studies have provided information to assess taxonomic boundaries, inform listing decisions made under the Endangered Species Act, identify unique or genetically depauperate populations, estimate population size or survival rates, develop management or recovery plans, breed wildlife in captivity, relocate wildlife from one location to another, and assess the effects of environmental change.

Deadlock-free genetic scheduling algorithm for automated manufacturing systems based on deadlock control policy.

PubMed

Xing, KeYi; Han, LiBin; Zhou, MengChu; Wang, Feng

2012-06-01

Deadlock-free control and scheduling are vital for optimizing the performance of automated manufacturing systems (AMSs) with shared resources and route flexibility. Based on the Petri net models of AMSs, this paper embeds the optimal deadlock avoidance policy into the genetic algorithm and develops a novel deadlock-free genetic scheduling algorithm for AMSs. A possible solution of the scheduling problem is coded as a chromosome representation that is a permutation with repetition of parts. By using the one-step look-ahead method in the optimal deadlock control policy, the feasibility of a chromosome is checked, and infeasible chromosomes are amended into feasible ones, which can be easily decoded into a feasible deadlock-free schedule. The chromosome representation and polynomial complexity of checking and amending procedures together support the cooperative aspect of genetic search for scheduling problems strongly.

Breed-Predispositions to Cancer in Pedigree Dogs

PubMed Central

Dobson, Jane M.

2013-01-01

Cancer is a common problem in dogs and although all breeds of dog and crossbred dogs may be affected, it is notable that some breeds of pedigree dogs appear to be at increased risk of certain types of cancer suggesting underlying genetic predisposition to cancer susceptibility. Although the aetiology of most cancers is likely to be multifactorial, the limited genetic diversity seen in purebred dogs facilitates genetic linkage or association studies on relatively small populations as compared to humans, and by using newly developed resources, genome-wide association studies in dog breeds are proving to be a powerful tool for unravelling complex disorders. This paper will review the literature on canine breed susceptibility to histiocytic sarcoma, osteosarcoma, haemangiosarcoma, mast cell tumours, lymphoma, melanoma, and mammary tumours including the recent advances in knowledge through molecular genetic, cytogenetic, and genome wide association studies. PMID:23738139

Review: Genetically modified plants for the promotion of human health.

PubMed

Yonekura-Sakakibara, Keiko; Saito, Kazuki

2006-12-01

Plants are attractive biological resources because of their ability to produce a huge variety of chemical compounds, and the familiarity of production in even the most rural settings. Genetic engineering gives plants additional characteristics and value for cultivation and post-harvest. Genetically modified (GM) plants of the "first generation" were conferred with traits beneficial to producers, whereas GM plants in subsequent "generations" are intended to provide beneficial traits for consumers. Golden Rice is a promising example of a GM plant in the second generation, and has overcome a number of obstacles for practical use. Furthermore, consumer-acceptable plants with health-promoting properties that are genetically modified using native genes are being developed. The emerging technology of metabolomics will also support the commercial realization of GM plants by providing comprehensive analyzes of plant biochemical components.

Genetics of Bone Density

MedlinePlus

... Record Research & Training Medical Research Initiatives Science Highlights Science Education Research in NIH Labs & Clinics Training Opportunities Library Resources Research Resources Clinical Research Resources Safety, Regulation ...

Genetic Counseling

MedlinePlus

... Testing Evaluating Genomic Tests Epidemiology Pathogen Genomics Resources Genetic Counseling Recommend on Facebook Tweet Share Compartir In ... informed decisions about testing and treatment. Reasons for Genetic Counseling There are many reasons that people go ...

Returning Individual Research Results: Development of a Cancer Genetics Education and Risk Communication Protocol

PubMed Central

Roberts, J. Scott; Shalowitz, David I.; Christensen, Kurt D.; Everett, Jessica N.; Kim, Scott Y. H.; Raskin, Leon; Gruber, Stephen B.

2011-01-01

The obligations of researchers to disclose clinically and/or personally significant individual research results are highly debated, but few empirical studies have addressed this topic. We describe the development of a protocol for returning research results to participants at one site of a multicenter study of the genetic epidemiology of melanoma. Protocol development involved numerous challenges: (1) deciding whether genotype results merited disclosure; (2) achieving an appropriate format for communicating results; (3) developing education materials; (4) deciding whether to retest samples for additional laboratory validation; (5) identifying and notifying selected participants; and (6) assessing the impact of disclosure. Our experience suggests potential obstacles depending on researcher resources and the design of the parent study, but offers a process by which researchers can responsibly return individual study results and evaluate the impact of disclosure. PMID:20831418

A Review of Living Collections with Special Emphasis on Sustainability and Its Impact on Research Across Multiple Disciplines

PubMed Central

2017-01-01

Formal living collections have unique characteristics that distinguish them from other types of biorepositories. Comprising diverse resources, microbe culture collections, crop and biodiversity plant germplasm collections, and animal germplasm repositories are commonly allied with specific research communities or stakeholder groups. Among living collections, microbial culture collections have very long and unique life histories, with some being older than 100 years. Regulatory, financial, and technical developments have impacted living collections in many ways. International treaty obligations and restrictions on release of genetically modified organisms complicate the activities of living collections. Funding for living collections is a continuing challenge and threatens to create a two-tier system where medically relevant collections are well funded and all other collections are underfunded and hence understaffed. Molecular, genetic, and whole genome sequence analysis of contents of microbes and other living resource collections bring additional value to living collections. PMID:27869477

A Review of Living Collections with Special Emphasis on Sustainability and Its Impact on Research Across Multiple Disciplines.

PubMed

McCluskey, Kevin

2017-02-01

Formal living collections have unique characteristics that distinguish them from other types of biorepositories. Comprising diverse resources, microbe culture collections, crop and biodiversity plant germplasm collections, and animal germplasm repositories are commonly allied with specific research communities or stakeholder groups. Among living collections, microbial culture collections have very long and unique life histories, with some being older than 100 years. Regulatory, financial, and technical developments have impacted living collections in many ways. International treaty obligations and restrictions on release of genetically modified organisms complicate the activities of living collections. Funding for living collections is a continuing challenge and threatens to create a two-tier system where medically relevant collections are well funded and all other collections are underfunded and hence understaffed. Molecular, genetic, and whole genome sequence analysis of contents of microbes and other living resource collections bring additional value to living collections.

Next generation DNA sequencing technology delivers valuable genetic markers for the genomic orphan legume species, Bituminaria bituminosa

PubMed Central

2011-01-01

Background Bituminaria bituminosa is a perennial legume species from the Canary Islands and Mediterranean region that has potential as a drought-tolerant pasture species and as a source of pharmaceutical compounds. Three botanical varieties have previously been identified in this species: albomarginata, bituminosa and crassiuscula. B. bituminosa can be considered a genomic 'orphan' species with very few genomic resources available. New DNA sequencing technologies provide an opportunity to develop high quality molecular markers for such orphan species. Results 432,306 mRNA molecules were sampled from a leaf transcriptome of a single B. bituminosa plant using Roche 454 pyrosequencing, resulting in an average read length of 345 bp (149.1 Mbp in total). Sequences were assembled into 3,838 isotigs/contigs representing putatively unique gene transcripts. Gene ontology descriptors were identified for 3,419 sequences. Raw sequence reads containing simple sequence repeat (SSR) motifs were identified, and 240 primer pairs flanking these motifs were designed. Of 87 primer pairs developed this way, 75 (86.2%) successfully amplified primarily single fragments by PCR. Fragment analysis using 20 primer pairs in 79 accessions of B. bituminosa detected 130 alleles at 21 SSR loci. Genetic diversity analyses confirmed that variation at these SSR loci accurately reflected known taxonomic relationships in original collections of B. bituminosa and provided additional evidence that a division of the botanical variety bituminosa into two according to geographical origin (Mediterranean region and Canary Islands) may be appropriate. Evidence of cross-pollination was also found between botanical varieties within a B. bituminosa breeding programme. Conclusions B. bituminosa can no longer be considered a genomic orphan species, having now a large (albeit incomplete) repertoire of expressed gene sequences that can serve as a resource for future genetic studies. This experimental approach was effective in developing codominant and polymorphic SSR markers for application in diverse genetic studies. These markers have already given new insight into genetic variation in B. bituminosa, providing evidence that a division of the botanical variety bituminosa may be appropriate. This approach is commended to those seeking to develop useful markers for genomic orphan species. PMID:22171578

Incorporating Social Media into your Support Tool Box: Points to Consider from Genetics-Based Communities.

PubMed

Rocha, Heather Mae; Savatt, Juliann M; Riggs, Erin Rooney; Wagner, Jennifer K; Faucett, W Andrew; Martin, Christa Lese

2018-04-01

Patients with newly-described or rare genetic findings are turning to social media to find and connect with others. Blogs, Facebook groups, and Twitter have all been reported as tools for patients to connect with one another. However, the preferences for social media use and privacy among patients, their families, and these communities have not been well characterized. To explore preferences about privacy and membership guidelines, an online survey was administered to two web-based patient registries, Simons Variation in Individuals Project ( www.simonsvipconnect.org ) and GenomeConnect ( www.genomeconnect.org ). Over a three-month period, invitations were sent to 2524 individuals and 103 responses (4%) were received and analyzed. Responses indicate that Facebook is the most popular resource accessed within this sample population (99%). Participants used social media to look for information about their diagnosis or test results (83%), read posts from rare disease groups or organizations (73%), participate in conversations about their diagnosis (67%), and connect with others to find support (58%). Focusing on privacy issues in social media, respondents indicate that membership and access impact the level of comfort in sharing personal or medical information. Nearly 60% of respondents felt uncomfortable sharing photos or medical information within a public Facebook group, whereas only 12% of respondents felt uncomfortable sharing in private group targeted to families alone. Using this preliminary data concerning social media use and privacy, we developed points for genetic counselors to incorporate when discussing available support resources for patients with a new, or rare, genetic diagnosis or genetic test result. Genetic counselors are trained to provide anticipatory guidance to families adapting to new genetic information, and are well-equipped to help patients consider their preferences about using social media as a source of information and support.

Population genetics of Sargassum horneri (Fucales, Phaeophyta) in China revealed by ISSR and SRAP markers

NASA Astrophysics Data System (ADS)

Yu, Shenhui; Chong, Zhuo; Zhao, Fengjuan; Yao, Jianting; Duan, Delin

2013-05-01

Sargassum horneri is a common brown macro-alga that is found in the inter-tidal ecosystems of China. To investigate the current status of seaweed resources and provide basic data for its sustainable development, ISSR (inter simple sequence repeat) and SRAP (sequence related amplified polymorphism) markers were used to analyze the population genetics among nine natural populations of S. horneri. The nine studied populations were distributed over 2 000 km from northeast to south China. The percentage of polymorphic loci P % (ISSR, 99.44%; SRAP, 100.00%), Nei's genetic diversity H (ISSR, 0.107-0.199; SRAP, 0.100-0.153), and Shannon's information index I (ISSR, 0.157-0.291; SRAP, 0.148-0.219) indicated a fair amount of genetic variability among the nine populations. Moreover, the high degree of gene differentiation G st (ISSR, 0.654; SRAP, 0.718) and low gene flow N m (ISSR, 0.265; SRAP, 0.196) implied that there was significant among-population differentiation, possibly as a result of habitat fragmentation. The matrices of genetic distances and fixation indices ( F st) among the populations correlated well with their geographical distribution (Mantel test R =0.541 5, 0.541 8; P =0.005 0, 0.002 0 and R =0.728 6, 0.641 2; P =0.001 0, 0.001 0, respectively); the Rongcheng population in the Shandong peninsula was the only exception. Overall, the genetic differentiation agreed with the geographic isolation. The fair amount of genetic diversity that was revealed in the S. horneri populations in China indicated that the seaweed resources had not been seriously affected by external factors.

Genetic Structure and Selection of a Core Collection for Long Term Conservation of Avocado in Mexico

PubMed Central

Guzmán, Luis F.; Machida-Hirano, Ryoko; Borrayo, Ernesto; Cortés-Cruz, Moisés; Espíndola-Barquera, María del Carmen; Heredia García, Elena

2017-01-01

Mexico, as the center of origin of avocado (Persea americama Mill.), harbors a wide genetic diversity of this species, whose identification may provide the grounds to not only understand its unique population structure and domestication history, but also inform the efforts aimed at its conservation. Although molecular characterization of cultivated avocado germplasm has been studied by several research groups, this had not been the case in Mexico. In order to elucidate the genetic structure of avocado in Mexico and the sustainable use of its genetic resources, 318 avocado accessions conserved in the germplasm collection in the National Avocado Genebank were analyzed using 28 markers [9 expressed sequence tag-Simple Sequence Repeats (SSRs) and 19 genomic SSRs]. Deviation from Hardy Weinberg Equilibrium and high inter-locus linkage disequilibrium were observed especially in drymifolia, and guatemalensis. Total averages of the observed and expected heterozygosity were 0.59 and 0.75, respectively. Although clear genetic differentiation was not observed among 3 botanical races: americana, drymifolia, and guatemalensis, the analyzed Mexican population can be classified into two groups that correspond to two different ecological regions. We developed a core-collection by K-means clustering method. The selected 36 individuals as core-collection successfully represented more than 80% of total alleles and showed heterozygosity values equal to or higher than those of the original collection, despite its constituting slightly more than 10% of the latter. Accessions selected as members of the core collection have now become candidates to be introduced in cryopreservation implying a minimum loss of genetic diversity and a back-up for existing field collections of such important genetic resources. PMID:28286510

Microsatellite isolation and marker development in carrot - genomic distribution, linkage mapping, genetic diversity analysis and marker transferability across Apiaceae

USDA-ARS?s Scientific Manuscript database

The Apiaceae family includes several vegetable and spice crop species among which carrot is the most economically important member, with ~21 million tons produced yearly worldwide. Despite its importance, molecular resources in this species are relatively underdeveloped. The availability of informat...

Learning about Genetic Engineering in an Outreach Laboratory: Influence of Motivation and Gender on Students' Cognitive Achievement

ERIC Educational Resources Information Center

Goldschmidt, Marlen; Bogner, Franz X.

2016-01-01

During the last 10 years, outreach science laboratories have become increasingly popular due to resource and time limitations in schools. Outreach laboratories offer hands-on projects in a situated and authentic learning setting, thereby promoting the development of students' scientific literacy. However, students' cognitive achievement within…

Creating a cryobank for germplasm of fruit and berry crops: methodological recommendations

USDA-ARS?s Scientific Manuscript database

Plant genetic resources are a national treasure in each country. They serve as a basis for developing new and improving existing varieties of plants. In Kazakhstan, a wide selection of cultivated and wild forms grow unique fruit and berry crops, including apple (Malus sieversii (Ledeb.) M. Roem., Ma...

A unified SNP map of sunflower (Helianthus annuus L.) derived from current genomic resources

USDA-ARS?s Scientific Manuscript database

Dense genetic maps are critical tools for plant breeders and geneticists. While many maps have been developed for sunflower in the last few decades, most have been based on low-throughput technologies and include markers numbers in the hundreds. However, two maps with reasonably dense coverage of a...

Growth

Treesearch

John R. Jones; George A. Schier

1985-01-01

This chapter considers aspen growth as a process, and discusses some characteristics of the growth and development of trees and stands. For the most part, factors affecting growth are discussed elsewhere, particularly in the GENETICS AND VARIATION chapter and in chapters in PART 11. ECOLOGY. Aspen growth as it relates to wood production is examined in the WOOD RESOURCE...

Development of knowledge and tools to enhance resilience of beef grazing systems for sustainable animal protein production

USDA-ARS?s Scientific Manuscript database

Ruminant livestock provide an important source of meat and dairy protein that sustain the health and livelihoods for much of the world’s population. Grazinglands that support ruminant livestock provide numerous other ecosystem services, including provision of food, water, and genetic resources; regu...

Sequencing of 15,622 gene-bearing BACs clarifies the gene-dense regions of the barley genome

USDA-ARS?s Scientific Manuscript database

Barley (Hordeum vulgare L.) possesses a large and highly repetitive genome of 5.1 Gb that has hindered the development of a complete sequence. In 2012, the International Barley Sequencing Consortium released a resource integrating whole-genome shotgun sequences with a physical and genetic framework....

Ensembl Genomes 2016: more genomes, more complexity.

PubMed

Kersey, Paul Julian; Allen, James E; Armean, Irina; Boddu, Sanjay; Bolt, Bruce J; Carvalho-Silva, Denise; Christensen, Mikkel; Davis, Paul; Falin, Lee J; Grabmueller, Christoph; Humphrey, Jay; Kerhornou, Arnaud; Khobova, Julia; Aranganathan, Naveen K; Langridge, Nicholas; Lowy, Ernesto; McDowall, Mark D; Maheswari, Uma; Nuhn, Michael; Ong, Chuang Kee; Overduin, Bert; Paulini, Michael; Pedro, Helder; Perry, Emily; Spudich, Giulietta; Tapanari, Electra; Walts, Brandon; Williams, Gareth; Tello-Ruiz, Marcela; Stein, Joshua; Wei, Sharon; Ware, Doreen; Bolser, Daniel M; Howe, Kevin L; Kulesha, Eugene; Lawson, Daniel; Maslen, Gareth; Staines, Daniel M

2016-01-04

Ensembl Genomes (http://www.ensemblgenomes.org) is an integrating resource for genome-scale data from non-vertebrate species, complementing the resources for vertebrate genomics developed in the context of the Ensembl project (http://www.ensembl.org). Together, the two resources provide a consistent set of programmatic and interactive interfaces to a rich range of data including reference sequence, gene models, transcriptional data, genetic variation and comparative analysis. This paper provides an update to the previous publications about the resource, with a focus on recent developments. These include the development of new analyses and views to represent polyploid genomes (of which bread wheat is the primary exemplar); and the continued up-scaling of the resource, which now includes over 23 000 bacterial genomes, 400 fungal genomes and 100 protist genomes, in addition to 55 genomes from invertebrate metazoa and 39 genomes from plants. This dramatic increase in the number of included genomes is one part of a broader effort to automate the integration of archival data (genome sequence, but also associated RNA sequence data and variant calls) within the context of reference genomes and make it available through the Ensembl user interfaces. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

Ensembl Genomes 2016: more genomes, more complexity

PubMed Central

Kersey, Paul Julian; Allen, James E.; Armean, Irina; Boddu, Sanjay; Bolt, Bruce J.; Carvalho-Silva, Denise; Christensen, Mikkel; Davis, Paul; Falin, Lee J.; Grabmueller, Christoph; Humphrey, Jay; Kerhornou, Arnaud; Khobova, Julia; Aranganathan, Naveen K.; Langridge, Nicholas; Lowy, Ernesto; McDowall, Mark D.; Maheswari, Uma; Nuhn, Michael; Ong, Chuang Kee; Overduin, Bert; Paulini, Michael; Pedro, Helder; Perry, Emily; Spudich, Giulietta; Tapanari, Electra; Walts, Brandon; Williams, Gareth; Tello–Ruiz, Marcela; Stein, Joshua; Wei, Sharon; Ware, Doreen; Bolser, Daniel M.; Howe, Kevin L.; Kulesha, Eugene; Lawson, Daniel; Maslen, Gareth; Staines, Daniel M.

2016-01-01

Ensembl Genomes (http://www.ensemblgenomes.org) is an integrating resource for genome-scale data from non-vertebrate species, complementing the resources for vertebrate genomics developed in the context of the Ensembl project (http://www.ensembl.org). Together, the two resources provide a consistent set of programmatic and interactive interfaces to a rich range of data including reference sequence, gene models, transcriptional data, genetic variation and comparative analysis. This paper provides an update to the previous publications about the resource, with a focus on recent developments. These include the development of new analyses and views to represent polyploid genomes (of which bread wheat is the primary exemplar); and the continued up-scaling of the resource, which now includes over 23 000 bacterial genomes, 400 fungal genomes and 100 protist genomes, in addition to 55 genomes from invertebrate metazoa and 39 genomes from plants. This dramatic increase in the number of included genomes is one part of a broader effort to automate the integration of archival data (genome sequence, but also associated RNA sequence data and variant calls) within the context of reference genomes and make it available through the Ensembl user interfaces. PMID:26578574

The CDC Hemophilia B mutation project mutation list: a new online resource.

PubMed

Li, Tengguo; Miller, Connie H; Payne, Amanda B; Craig Hooper, W

2013-11-01

Hemophilia B (HB) is caused by mutations in the human gene F9. The mutation type plays a pivotal role in genetic counseling and prediction of inhibitor development. To help the HB community understand the molecular etiology of HB, we have developed a listing of all F9 mutations that are reported to cause HB based on the literature and existing databases. The Centers for Disease Control and Prevention (CDC) Hemophilia B Mutation Project (CHBMP) mutation list is compiled in an easily accessible format of Microsoft Excel and contains 1083 unique mutations that are reported to cause HB. Each mutation is identified using Human Genome Variation Society (HGVS) nomenclature standards. The mutation types and the predicted changes in amino acids, if applicable, are also provided. Related information including the location of mutation, severity of HB, the presence of inhibitor, and original publication reference are listed as well. Therefore, our mutation list provides an easily accessible resource for genetic counselors and HB researchers to predict inhibitors. The CHBMP mutation list is freely accessible at http://www.cdc.gov/hemophiliamutations.

HapZipper: sharing HapMap populations just got easier.

PubMed

Chanda, Pritam; Elhaik, Eran; Bader, Joel S

2012-11-01

The rapidly growing amount of genomic sequence data being generated and made publicly available necessitate the development of new data storage and archiving methods. The vast amount of data being shared and manipulated also create new challenges for network resources. Thus, developing advanced data compression techniques is becoming an integral part of data production and analysis. The HapMap project is one of the largest public resources of human single-nucleotide polymorphisms (SNPs), characterizing over 3 million SNPs genotyped in over 1000 individuals. The standard format and biological properties of HapMap data suggest that a dedicated genetic compression method can outperform generic compression tools. We propose a compression methodology for genetic data by introducing HapZipper, a lossless compression tool tailored to compress HapMap data beyond benchmarks defined by generic tools such as gzip, bzip2 and lzma. We demonstrate the usefulness of HapZipper by compressing HapMap 3 populations to <5% of their original sizes. HapZipper is freely downloadable from https://bitbucket.org/pchanda/hapzipper/downloads/HapZipper.tar.bz2.

Lupus - resources

MedlinePlus

Resources - lupus ... The following organizations are good resources for information on systemic lupus erythematosus : Genetics Home Reference -- ghr.nlm.nih.gov/condition/systemic-lupus-erythematosus Lupus Foundation of America -- ...

Genetic variation and gene expression across multiple tissues and developmental stages in a nonhuman primate.

PubMed

Jasinska, Anna J; Zelaya, Ivette; Service, Susan K; Peterson, Christine B; Cantor, Rita M; Choi, Oi-Wa; DeYoung, Joseph; Eskin, Eleazar; Fairbanks, Lynn A; Fears, Scott; Furterer, Allison E; Huang, Yu S; Ramensky, Vasily; Schmitt, Christopher A; Svardal, Hannes; Jorgensen, Matthew J; Kaplan, Jay R; Villar, Diego; Aken, Bronwen L; Flicek, Paul; Nag, Rishi; Wong, Emily S; Blangero, John; Dyer, Thomas D; Bogomolov, Marina; Benjamini, Yoav; Weinstock, George M; Dewar, Ken; Sabatti, Chiara; Wilson, Richard K; Jentsch, J David; Warren, Wesley; Coppola, Giovanni; Woods, Roger P; Freimer, Nelson B

2017-12-01

By analyzing multitissue gene expression and genome-wide genetic variation data in samples from a vervet monkey pedigree, we generated a transcriptome resource and produced the first catalog of expression quantitative trait loci (eQTLs) in a nonhuman primate model. This catalog contains more genome-wide significant eQTLs per sample than comparable human resources and identifies sex- and age-related expression patterns. Findings include a master regulatory locus that likely has a role in immune function and a locus regulating hippocampal long noncoding RNAs (lncRNAs), whose expression correlates with hippocampal volume. This resource will facilitate genetic investigation of quantitative traits, including brain and behavioral phenotypes relevant to neuropsychiatric disorders.

A Model for the Development of Web-Based, Student-Centered Science Education Resources.

ERIC Educational Resources Information Center

Murfin, Brian; Go, Vanessa

The purpose of this study was to evaluate The Student Genome Project, an experiment in web-based genetics education. Over a two-year period, a team from New York University worked with a biology teacher and 33 high school students (N=33), and a middle school science teacher and a class of students (N=21) to develop a World Wide Web site intended…

C++ Planning and Resource Reasoning (PARR) shell

NASA Technical Reports Server (NTRS)

Mcintyre, James; Tuchman, Alan; Mclean, David; Littlefield, Ronald

1994-01-01

This paper describes a generic, C++ version of the Planning and Resource Reasoning (PARR) shell which has been developed to supersede the C-based versions of PARR that are currently used to support AI planning and scheduling applications in flight operations centers at Goddard Space Flight Center. This new object-oriented version of PARR can be more easily customized to build a variety of planning and scheduling applications, and C++ PARR applications can be more easily ported to different environments. Genetic classes, constraints, strategies, and paradigms are described along with two types of PARR interfaces.

Biomedical databases: protecting privacy and promoting research.

PubMed

Wylie, Jean E; Mineau, Geraldine P

2003-03-01

When combined with medical information, large electronic databases of information that identify individuals provide superlative resources for genetic, epidemiology and other biomedical research. Such research resources increasingly need to balance the protection of privacy and confidentiality with the promotion of research. Models that do not allow the use of such individual-identifying information constrain research; models that involve commercial interests raise concerns about what type of access is acceptable. Researchers, individuals representing the public interest and those developing regulatory guidelines must be involved in an ongoing dialogue to identify practical models.

Molecular Genetic Testing in Reward Deficiency Syndrome (RDS): Facts and Fiction.

PubMed

Blum, Kenneth; Badgaiyan, Rajendra D; Agan, Gozde; Fratantonio, James; Simpatico, Thomas; Febo, Marcelo; Haberstick, Brett C; Smolen, Andrew; Gold, Mark S

The Brain Reward Cascade (BRC) is an interaction of neurotransmitters and their respective genes to control the amount of dopamine released within the brain. Any variations within this pathway, whether genetic or environmental (epigenetic), may result in addictive behaviors or RDS, which was coined to define addictive behaviors and their genetic components. To carry out this review we searched a number of important databases including: Filtered: Cochrane Systematic reviews; DARE; Pubmed Central Clinical Quaries; National Guideline Clearinghouse and unfiltered resources: PsychINFO; ACP PIER; PsychSage; Pubmed/Medline. The major search terms included: dopamine agonist therapy for Addiction; dopamine agonist therapy for Reward dependence; dopamine antagonistic therapy for addiction; dopamine antagonistic therapy for reward dependence and neurogenetics of RDS. While there are many studies claiming a genetic association with RDS behavior, not all are scientifically accurate. Albeit our bias, this Clinical Pearl discusses the facts and fictions behind molecular genetic testing in RDS and the significance behind the development of the Genetic Addiction Risk Score (GARS PREDX ™), the first test to accurately predict one's genetic risk for RDS.

Pre-breeding for diversification of primary gene pool and genetic enhancement of grain legumes

PubMed Central

Sharma, Shivali; Upadhyaya, H. D.; Varshney, R. K.; Gowda, C. L. L.

2013-01-01

The narrow genetic base of cultivars coupled with low utilization of genetic resources are the major factors limiting grain legume production and productivity globally. Exploitation of new and diverse sources of variation is needed for the genetic enhancement of grain legumes. Wild relatives with enhanced levels of resistance/tolerance to multiple stresses provide important sources of genetic diversity for crop improvement. However, their exploitation for cultivar improvement is limited by cross-incompatibility barriers and linkage drags. Pre-breeding provides a unique opportunity, through the introgression of desirable genes from wild germplasm into genetic backgrounds readily used by the breeders with minimum linkage drag, to overcome this. Pre-breeding activities using promising landraces, wild relatives, and popular cultivars have been initiated at International Crops Research Institute for the Semi-Arid Tropics (ICRISAT) to develop new gene pools in chickpea, pigeonpea, and groundnut with a high frequency of useful genes, wider adaptability, and a broad genetic base. The availability of molecular markers will greatly assist in reducing linkage drags and increasing the efficiency of introgression in pre-breeding programs. PMID:23970889

A MULTI-LOCUS, MULTI-TAXA PHYLOGEOGRAPHICAL ANALYSIS OF GENETIC DIVERSITY

EPA Science Inventory

In addition to measuring spatial patterns of genetic diversity, population genetic measures of biological resources should include temporal data that indicate whether the observed patterns are the result of historical or contemporary processes. In general, genetic measures focus...

Development of new SNP derived cleaved amplified polymorphic sequence marker set and its successful utilization in the genetic analysis of seed color variation in barley.

PubMed

Bungartz, Annemarie; Klaus, Marius; Mathew, Boby; Léon, Jens; Naz, Ali Ahmad

2016-03-01

The aim of the present study was to develop a new cost effective PCR based CAPS marker set using advantages of high-throughput SNP genotyping. Initially, SNP survey was made using 20 diverse barley genotypes via 9k iSelect array genotyping that resulted in 6334 polymorphic SNP markers. Principle component analysis using this marker data showed fine differentiation of barley diverse gene pool. Till this end, we developed 200 SNP derived CAPS markers distributed across the genome covering around 991cM with an average marker density of 5.09cM. Further, we genotyped 68 CAPS markers in an F2 population (Cheri×ICB181160) segregating for seed color variation in barley. Genetic mapping of seed color revealed putative linkage of single nuclear gene on chromosome 1H. These findings showed the proof of concept for the development and utility of a newer cost effective genomic tool kit to analyze broader genetic resources of barley worldwide. Copyright © 2016 Elsevier Inc. All rights reserved.

Prioritization of Malus accessions for collection cryopreservation at the USDA-ARS National Center for Genetic Resources Preservation

USDA-ARS?s Scientific Manuscript database

The USDA-ARS National Plant Germplasm System maintains a grafted collection of apple accessions representing 49 taxa in Geneva, NY. Dormant buds of many of these accessions have been routinely cryopreserved at the USDA-ARS National Center for Genetic Resources Preservation (NCGRP) in Fort Collins, C...

Construction of a high-density American cranberry (Vaccinium macrocarpon Ait.) composite map using genotyping-by-sequencing for multi-pedigree linkage mapping

USDA-ARS?s Scientific Manuscript database

The American cranberry (Vaccinium macrocarpon Ait.) is a recently domesticated, but economically important, fruit crop with limited molecular resources. New genetic resources could accelerate genetic gain in cranberry through characterization of its genomic structure and by enabling molecular-assist...

Integration of genomic resources to uncover pleiotropic regions associated with age at puberty and reproductive longevity in sows

USDA-ARS?s Scientific Manuscript database

Commercial and experimental genetic resources were used to investigate genetic pleiotropic factors that influence age at puberty, litter-size and reproductive longevity. The phenotypes were complemented by high-density genotyping and whole genome and RNA sequencing. The SNPs from Porcine SNP60 BeadA...

U.S. Sorghum genetic resources collection: 15 years of progress (2001-2016)

USDA-ARS?s Scientific Manuscript database

The U.S. sorghum genetic resources collection at Griffin, GA, is one of the largest collections in the National Plant Germplasm System. In 2001, improved maintenance was greatly needed as accessions weren’t regenerated routinely, viability tests weren’t conducted, and most seed was stored in 4C inst...

Why preserve and evaluate genetic resources in peanut?

USDA-ARS?s Scientific Manuscript database

Peanuts are produced in more than 100 countries with a total global total production in 2010 of 37,953,949 metric tons (FAO statistics, 2010). Because peanut is an important crop, it is imperative that its germplasm be preserved in order to conserve the genetic diversity and provide a resource to i...

Large-Scale SNP Discovery and Genotyping for Constructing a High-Density Genetic Map of Tea Plant Using Specific-Locus Amplified Fragment Sequencing (SLAF-seq)

PubMed Central

Ma, Chun-Lei; Jin, Ji-Qiang; Li, Chun-Fang; Wang, Rong-Kai; Zheng, Hong-Kun; Yao, Ming-Zhe; Chen, Liang

2015-01-01

Genetic maps are important tools in plant genomics and breeding. The present study reports the large-scale discovery of single nucleotide polymorphisms (SNPs) for genetic map construction in tea plant. We developed a total of 6,042 valid SNP markers using specific-locus amplified fragment sequencing (SLAF-seq), and subsequently mapped them into the previous framework map. The final map contained 6,448 molecular markers, distributing on fifteen linkage groups corresponding to the number of tea plant chromosomes. The total map length was 3,965 cM, with an average inter-locus distance of 1.0 cM. This map is the first SNP-based reference map of tea plant, as well as the most saturated one developed to date. The SNP markers and map resources generated in this study provide a wealth of genetic information that can serve as a foundation for downstream genetic analyses, such as the fine mapping of quantitative trait loci (QTL), map-based cloning, marker-assisted selection, and anchoring of scaffolds to facilitate the process of whole genome sequencing projects for tea plant. PMID:26035838

Storytellers as partners in developing a genetics education resource for health professionals

PubMed Central

Kirk, Maggie; Tonkin, Emma; Skirton, Heather; McDonald, Kevin; Cope, Buddug; Morgan, Rhian

2013-01-01

Summary Advances in genetics are bringing unprecedented opportunities for understanding health and disease, developing new therapies and changes in healthcare practice. Many nurses and midwives lack competence and confidence in integrating genetics into professional practice. One approach to enhance understanding of genetics is to simulate clinical exposure through storytelling. Stories are acknowledged as a powerful learning tool, being understandable and memorable, stimulating critical thinking, and linking theory to practice. Telling Stories, Understanding Real Life Genetics is a freely accessible website that sets people's stories within an education framework. The links between the stories and professional practice are made explicit and additional features support learning and teaching. Care of the storytellers within an ethical framework is of paramount importance. Storytellers are viewed as partners in the project. The challenges encountered include preserving the authentic voice and dignity of the storyteller. Project team members have also experienced ‘professional shame’ when negative experiences have been recounted, and the stories have had an impact on the team. The experience of working with storytellers has been positive. The storytellers want to be heard so that others will benefit from their stories. They serve as a reminder of why this work is important. PMID:22197414

Enriching Genomic Resources and Marker Development from Transcript Sequences of Jatropha curcas for Microgravity Studies

PubMed Central

Tian, Wenlan; Paudel, Dev

2017-01-01

Jatropha (Jatropha curcas L.) is an economically important species with a great potential for biodiesel production. To enrich the jatropha genomic databases and resources for microgravity studies, we sequenced and annotated the transcriptome of jatropha and developed SSR and SNP markers from the transcriptome sequences. In total 1,714,433 raw reads with an average length of 441.2 nucleotides were generated. De novo assembling and clustering resulted in 115,611 uniquely assembled sequences (UASs) including 21,418 full-length cDNAs and 23,264 new jatropha transcript sequences. The whole set of UASs were fully annotated, out of which 59,903 (51.81%) were assigned with gene ontology (GO) term, 12,584 (10.88%) had orthologs in Eukaryotic Orthologous Groups (KOG), and 8,822 (7.63%) were mapped to 317 pathways in six different categories in Kyoto Encyclopedia of Genes and Genome (KEGG) database, and it contained 3,588 putative transcription factors. From the UASs, 9,798 SSRs were discovered with AG/CT as the most frequent (45.8%) SSR motif type. Further 38,693 SNPs were detected and 7,584 remained after filtering. This UAS set has enriched the current jatropha genomic databases and provided a large number of genetic markers, which can facilitate jatropha genetic improvement and many other genetic and biological studies. PMID:28154822

Development and Application of Genomic Resources in an Endangered Palaeoendemic Tree, Parrotia subaequalis (Hamamelidaceae) From Eastern China

PubMed Central

Zhang, Yun-Yan; Shi, En; Yang, Zhao-Ping; Geng, Qi-Fang; Qiu, Ying-Xiong; Wang, Zhong-Sheng

2018-01-01

Parrotia subaequalis is an endangered palaeoendemic tree from disjunct montane sites in eastern China. Due to the lack of effective genomic resources, the genetic diversity and population structure of this endangered species are not clearly understood. In this study, we conducted paired-end shotgun sequencing (2 × 125 bp) of genomic DNA for two individuals of P. subaequalis on the Illumina HiSeq platform. Based on the resulting sequences, we have successfully assembled the complete chloroplast genome of P. subaequalis, as well as identified the polymorphic chloroplast microsatellites (cpSSRs), nuclear microsatellites (nSSRs) and mutational hotspots of chloroplast. Ten polymorphic cpSSR loci and 12 polymorphic nSSR loci were used to genotype 96 individuals of P. subaequalis from six populations to estimate genetic diversity and population structure. Our results revealed that P. subaequalis exhibited abundant genetic diversity (e.g., cpSSRs: Hcp = 0.862; nSSRs: HT = 0.559) and high genetic differentiation (e.g., cpSSRs: RST = 0.652; nSSRs: RST = 0.331), and characterized by a low pollen-to-seed migration ratio (r ≈ 1.78). These genetic patterns are attributable to its long evolutionary histories and low levels of contemporary inter-population gene flow by pollen and seed. In addition, lack of isolation-by-distance pattern and strong population genetic structuring in both marker systems, suggests that long-term isolation and/or habitat fragmentation as well as genetic drift may have also contributed to the geographic differentiation of P. subaequalis. Therefore, long-term habitat protection is the most important methods to prevent further loss of genetic variation and a decrease in effective population size. Furthermore, both cpSSRs and nSSRs revealed that P. subaequalis populations consisted of three genetic clusters, which should be considered as separated conservation units. PMID:29545814

The Contribution of Buckwheat Genetic Resources to Health and Dietary Diversity

PubMed Central

Sytar, Oksana; Brestic, Marian; Zivcak, Marek; Tran, Lam-Son Phan

2016-01-01

Despite several reports on the beneficial effects of buckwheat in prevention of human diseases, little attention has been devoted to the variability of biochemical and physiological traits in different buckwheat genetic resources. This review describes the biochemical evaluation of buckwheat genetic resources and the identification of elite genotypes for plant breeding and exploitation. The various types of bioactive compounds present in different varieties provide basic background information needed for the efficient production of buckwheat foods with added value. In this review, we will provide an integrated view of the biochemistry of bioactive compounds of buckwheat plants of different origin, especially of fagopyrin, proteins and amino acids, as well as of other phenolic compounds including rutin and chlorogenic acid. In addition to the genetic background, the effect of different growth conditions is discussed. The health effects of fagopyrin, phenolic acids, specific proteins and rutin are also presented. PMID:27252586

Advances in Maize Genomics and Their Value for Enhancing Genetic Gains from Breeding

PubMed Central

Xu, Yunbi; Skinner, Debra J.; Wu, Huixia; Palacios-Rojas, Natalia; Araus, Jose Luis; Yan, Jianbing; Gao, Shibin; Warburton, Marilyn L.; Crouch, Jonathan H.

2009-01-01

Maize is an important crop for food, feed, forage, and fuel across tropical and temperate areas of the world. Diversity studies at genetic, molecular, and functional levels have revealed that, tropical maize germplasm, landraces, and wild relatives harbor a significantly wider range of genetic variation. Among all types of markers, SNP markers are increasingly the marker-of-choice for all genomics applications in maize breeding. Genetic mapping has been developed through conventional linkage mapping and more recently through linkage disequilibrium-based association analyses. Maize genome sequencing, initially focused on gene-rich regions, now aims for the availability of complete genome sequence. Conventional insertion mutation-based cloning has been complemented recently by EST- and map-based cloning. Transgenics and nutritional genomics are rapidly advancing fields targeting important agronomic traits including pest resistance and grain quality. Substantial advances have been made in methodologies for genomics-assisted breeding, enhancing progress in yield as well as abiotic and biotic stress resistances. Various genomic databases and informatics tools have been developed, among which MaizeGDB is the most developed and widely used by the maize research community. In the future, more emphasis should be given to the development of tools and strategic germplasm resources for more effective molecular breeding of tropical maize products. PMID:19688107

Information needs of mothers regarding communicating BRCA1/2 cancer genetic test results to their children.

PubMed

Tercyak, Kenneth P; Peshkin, Beth N; Demarco, Tiffani A; Patenaude, Andrea Farkas; Schneider, Katherine A; Garber, Judy E; Valdimarsdottir, Heiddis B; Schwartz, Marc D

2007-01-01

Mothers who participate in genetic testing for hereditary breast/ovarian cancer risk must decide if, when, and how to ultimately share their BRCA1 and BRCA2 (BRCA1/2) test results with their minor-age children. One of the primary aides for mothers in making this decision is cancer genetic counseling. However, counseling is limited in how well it can educate mothers about such decisions without the availability of resources that are specific to family communication and genetic testing per se. In an effort to fill this gap and identify mothers most likely to benefit from such resources, surveys were conducted with 187 mothers undergoing BRCA1/2 testing who had children 8-21 years old. Data were collected weeks after genetic testing but prior to mothers' learning of their test results; quantitative assessments of informational resource needs (i.e., speaking with previous BRCA1/2 testing participants who are parents regarding their experiences, reading educational literature about options and what to expect, speaking with a family counselor, attending a family support group, and self-nominated other resources), testing motivations, decision making vigilance, and decisional conflict regarding communicating test results to children were included. Mothers' most-to-least frequently cited information resource needs were: literature (93.4%), family counseling (85.8%), prior participants (79.0%), support groups (53.9%), and other (28.9%; e.g., pediatricians and psychologists). Seventy-eight percent of mothers were interested in accessing three or more resources. In multivariate regression analyses, testing motivations (beta = 0.35, p = 0.03), decision-making vigilance (beta = 0.16, p = 0.00), and decisional conflict (beta = 0.10, p = 0.00) were associated with mothers' need level; mothers with a greater interest in testing to learn about their children's risks, those with more vigilant decision-making styles, and those with higher decisional conflict had the greatest need. In conjunction with enhanced genetic counseling focusing on family disclosure, educational literature, and psychosocial support may promote improved outcomes.

Genetics Home Reference: Blau syndrome

MedlinePlus

... inherited version of the disorder called early-onset sarcoidosis. Related Information What does it mean if a ... Genetic Testing Registry: Blau syndrome Genetic Testing Registry: Sarcoidosis, early-onset Other Diagnosis and Management Resources (2 ...

Genetics Home Reference: 3q29 microduplication syndrome

MedlinePlus

... 3q29 Related Information How are genetic conditions and genes named? Additional Information & Resources MedlinePlus (3 links) Encyclopedia: Microcephaly Encyclopedia: Obesity Health Topic: Developmental Disabilities Genetic and Rare Diseases ...

Genetic conservation and paddlefish propagation

USGS Publications Warehouse

Sloss, Brian L.; Klumb, Robert A.; Heist, Edward J.

2009-01-01

The conservation of genetic diversity of our natural resources is overwhelmingly one of the central foci of 21st century management practices. Three recommendations related to the conservation of paddlefish Polyodon spathula genetic diversity are to (1) identify genetic diversity at both nuclear and mitochondrial DNA loci using a suggested list of 20 sampling locations, (2) use genetic diversity estimates to develop genetic management units, and (3) identify broodstock sources to minimize effects of supplemental stocking on the genetic integrity of native paddlefish populations. We review previous genetic work on paddlefish and described key principles and concepts associated with maintaining genetic diversity within and among paddlefish populations and also present a genetic case study of current paddlefish propagation at the U.S. Fish and Wildlife Service Gavins Point National Fish Hatchery. This study confirmed that three potential sources of broodfish were genetically indistinguishable at the loci examined, allowing the management agencies cooperating on this program flexibility in sampling gametes. This study also showed significant bias in the hatchery occurred in terms of male reproductive contribution, which resulted in a shift in the genetic diversity of progeny compared to the broodfish. This shift was shown to result from differential male contributions, partially attributed to the mode of egg fertilization. Genetic insights enable implementation of a paddlefish propagation program within an adaptive management strategy that conserves inherent genetic diversity while achieving demographic goals.

Mining the human genome after Association for Molecular Pathology v. Myriad Genetics

PubMed Central

Evans, Barbara J

2014-01-01

The Supreme Court's recent decision in Association for Molecular Pathology v. Myriad Genetics portrays the human genome as a product of nature. This frames medical genetics as an extractive industry that mines a natural resource to produce valuable goods and services. Natural resource law offers insights into problems medical geneticists can expect after this decision and suggests possible solutions. Increased competition among clinical laboratories offers various benefits but threatens to increase fragmentation of genetic data resources, potentially causing waste in the form of lost opportunities to discover the clinical significance of particular gene variants. The solution lies in addressing legal barriers to appropriate data sharing. Sustainable discovery in the field of medical genetics can best be achieved through voluntary data sharing rather than command-and-control tactics, but voluntary mechanisms must be conceived broadly to include market-based approaches as well as donative and publicly funded data commons. The recently revised Health Insurance Portability and Accountability Act Privacy Rule offers an improved—but still imperfect—framework for market-oriented data sharing. This article explores strategies for addressing the Privacy Rule's remaining defects. America is close to having a legal framework that can reward innovators, protect privacy, and promote needed data sharing to advance medical genetics. Genet Med 16 7, 504–509. PMID:24357850

De novo transcriptome assembly, development of EST-SSR markers and population genetic analyses for the desert biomass willow, Salix psammophila

PubMed Central

Jia, Huixia; Yang, Haifeng; Sun, Pei; Li, Jianbo; Zhang, Jin; Guo, Yinghua; Han, Xiaojiao; Zhang, Guosheng; Lu, Mengzhu; Hu, Jianjun

2016-01-01

Salix psammophila, a sandy shrub known as desert willow, is regarded as a potential biomass feedstock and plays an important role in maintaining local ecosystems. However, a lack of genomic data and efficient molecular markers limit the study of its population evolution and genetic breeding. In this study, chromosome counts, flow cytometry and SSR analyses indicated that S. psammophila is tetraploid. A total of 6,346 EST-SSRs were detected based on 71,458 de novo assembled unigenes from transcriptome data. Twenty-seven EST-SSR markers were developed to evaluate the genetic diversity and population structure of S. psammophila from eight natural populations in Northern China. High levels of genetic diversity (mean 10.63 alleles per locus; mean HE 0.689) were dectected in S. psammophila. The weak population structure and little genetic differentiation (pairwise FST = 0.006–0.016) were found among Population 1-Population 7 (Pop1-Pop7; Inner Mongolia and Shaanxi), but Pop8 (Ningxia) was clearly separated from Pop1-Pop7 and moderate differentiation (pairwise FST = 0.045–0.055) was detected between them, which may be influenced by local habitat conditions. Molecular variance analyses indicated that most of the genetic variation (94.27%) existed within populations. These results provide valuable genetic informations for natural resource conservation and breeding programme optimisation of S. psammophila. PMID:27995985

Food security: increasing yield and improving resource use efficiency.

PubMed

Parry, Martin A J; Hawkesford, Malcolm J

2010-11-01

Food production and security will be a major issue for supplying an increasing world population. The problem will almost certainly be exacerbated by climate change. There is a projected need to double food production by 2050. In recent times, the trend has been for incremental modest yield increases for most crops. There is an urgent need to develop integrated and sustainable approaches that will significantly increase both production per unit land area and the resource use efficiency of crops. This review considers some key processes involved in plant growth and development with some examples of ways in which molecular technology, plant breeding and genetics may increase the yield and resource use efficiency of wheat. The successful application of biotechnology to breeding is essential to provide the major increases in production required. However, each crop and each specific agricultural situation presents specific requirements and targets for optimisation. Some increases in production will come about as new varieties are developed which are able to produce satisfactory crops on marginal land presently not considered appropriate for arable crops. Other new varieties will be developed to increase both yield and resource use efficiency on the best land.

Good laboratory practices for biochemical genetic testing and newborn screening for inherited metabolic disorders.

PubMed

2012-04-06

Biochemical genetic testing and newborn screening are essential laboratory services for the screening, detection, diagnosis, and monitoring of inborn errors of metabolism or inherited metabolic disorders. Under the Clinical Laboratory Improvement Amendments of 1988 (CLIA) regulations, laboratory testing is categorized on the basis of the level of testing complexity as either waived (i.e., from routine regulatory oversight) or nonwaived testing (which includes tests of moderate and high complexity). Laboratories that perform biochemical genetic testing are required by CLIA regulations to meet the general quality systems requirements for nonwaived testing and the personnel requirements for high-complexity testing. Laboratories that perform public health newborn screening are subject to the same CLIA regulations and applicable state requirements. As the number of inherited metabolic diseases that are included in state-based newborn screening programs continues to increase, ensuring the quality of performance and delivery of testing services remains a continuous challenge not only for public health laboratories and other newborn screening facilities but also for biochemical genetic testing laboratories. To help ensure the quality of laboratory testing, CDC collaborated with the Centers for Medicare & Medicaid Services, the Food and Drug Administration, the Health Resources and Services Administration, and the National Institutes of Health to develop guidelines for laboratories to meet CLIA requirements and apply additional quality assurance measures for these areas of genetic testing. This report provides recommendations for good laboratory practices that were developed based on recommendations from the Clinical Laboratory Improvement Advisory Committee, with additional input from the Secretary's Advisory Committee on Genetics, Health, and Society; the Secretary's Advisory Committee on Heritable Disorders in Newborns and Children; and representatives of newborn screening laboratories. The recommended practices address the benefits of using a quality management system approach, factors to consider before introducing new tests, establishment and verification of test performance specifications, the total laboratory testing process (which consists of the preanalytic, analytic, and postanalytic phases), confidentiality of patient information and test results, and personnel qualifications and responsibilities for laboratory testing for inherited metabolic diseases. These recommendations are intended for laboratories that perform biochemical genetic testing to improve the quality of laboratory services and for newborn screening laboratories to ensure the quality of laboratory practices for inherited metabolic disorders. These recommendations also are intended as a resource for medical and public health professionals who evaluate laboratory practices, for users of laboratory services to facilitate their collaboration with newborn screening systems and use of biochemical genetic tests, and for standard-setting organizations and professional societies in developing future laboratory quality standards and practice recommendations. This report complements Good Laboratory Practices for Molecular Genetic Testing for Heritable Diseases and Conditions (CDC. Good laboratory practices for molecular genetic testing for heritable diseases and conditions. MMWR 2009;58 [No. RR-6]) to provide guidance for ensuring and improving the quality of genetic laboratory services and public health outcomes. Future recommendations for additional areas of genetic testing will be considered on the basis of continued monitoring and evaluation of laboratory practices, technology advancements, and the development of laboratory standards and guidelines.

Dew inspired breathing-based detection of genetic point mutation visualized by naked eye

PubMed Central

Xie, Liping; Wang, Tongzhou; Huang, Tianqi; Hou, Wei; Huang, Guoliang; Du, Yanan

2014-01-01

A novel label-free method based on breathing-induced vapor condensation was developed for detection of genetic point mutation. The dew-inspired detection was realized by integration of target-induced DNA ligation with rolling circle amplification (RCA). The vapor condensation induced by breathing transduced the RCA-amplified variances in DNA contents into visible contrast. The image could be recorded by a cell phone for further or even remote analysis. This green assay offers a naked-eye-reading method potentially applied for point-of-care liver cancer diagnosis in resource-limited regions. PMID:25199907

Dew inspired breathing-based detection of genetic point mutation visualized by naked eye

NASA Astrophysics Data System (ADS)

Xie, Liping; Wang, Tongzhou; Huang, Tianqi; Hou, Wei; Huang, Guoliang; Du, Yanan

2014-09-01

A novel label-free method based on breathing-induced vapor condensation was developed for detection of genetic point mutation. The dew-inspired detection was realized by integration of target-induced DNA ligation with rolling circle amplification (RCA). The vapor condensation induced by breathing transduced the RCA-amplified variances in DNA contents into visible contrast. The image could be recorded by a cell phone for further or even remote analysis. This green assay offers a naked-eye-reading method potentially applied for point-of-care liver cancer diagnosis in resource-limited regions.

Dew inspired breathing-based detection of genetic point mutation visualized by naked eye.

PubMed

Xie, Liping; Wang, Tongzhou; Huang, Tianqi; Hou, Wei; Huang, Guoliang; Du, Yanan

2014-09-09

A novel label-free method based on breathing-induced vapor condensation was developed for detection of genetic point mutation. The dew-inspired detection was realized by integration of target-induced DNA ligation with rolling circle amplification (RCA). The vapor condensation induced by breathing transduced the RCA-amplified variances in DNA contents into visible contrast. The image could be recorded by a cell phone for further or even remote analysis. This green assay offers a naked-eye-reading method potentially applied for point-of-care liver cancer diagnosis in resource-limited regions.

DisGeNET-RDF: harnessing the innovative power of the Semantic Web to explore the genetic basis of diseases.

PubMed

Queralt-Rosinach, Núria; Piñero, Janet; Bravo, Àlex; Sanz, Ferran; Furlong, Laura I

2016-07-15

DisGeNET-RDF makes available knowledge on the genetic basis of human diseases in the Semantic Web. Gene-disease associations (GDAs) and their provenance metadata are published as human-readable and machine-processable web resources. The information on GDAs included in DisGeNET-RDF is interlinked to other biomedical databases to support the development of bioinformatics approaches for translational research through evidence-based exploitation of a rich and fully interconnected linked open data. http://rdf.disgenet.org/ support@disgenet.org. © The Author 2016. Published by Oxford University Press.

SoyBase, The USDA-ARS Soybean Genetics and Genomics Database

USDA-ARS?s Scientific Manuscript database

SoyBase, the USDA-ARS soybean genetic database, is a comprehensive repository for professionally curated genetics, genomics and related data resources for soybean. SoyBase contains the most current genetic, physical and genomic sequence maps integrated with qualitative and quantitative traits. The...

The development of 10 novel polymorphic microsatellite markers through next generation sequencing and a preliminary population genetic analysis for the endangered Glenelg spiny crayfish, Euastacus bispinosus.

PubMed

Miller, Adam D; Van Rooyen, Anthony; Sweeney, Oisín F; Whiterod, Nick S; Weeks, Andrew R

2013-07-01

The Glenelg spiny crayfish, Euastacus bispinosus, is an iconic freshwater invertebrate of south eastern Australia and listed as 'endangered' under the Environment Protection and Biodiversity Conservation Act 1999, and 'vulnerable' under the International Union for Conservation of Nature's Red List. The species has suffered major population declines as a result of over-fishing, low environmental flows, the introduction of invasive fish species and habitat degradation. In order to develop an effective conservation strategy, patterns of gene flow, genetic structure and genetic diversity across the species distribution need to be clearly understood. In this study we develop a suite of polymorphic microsatellite markers by next generation sequencing. A total of 15 polymorphic loci were identified and 10 characterized using 22 individuals from the lower Glenelg River. We observed low to moderate genetic variation across most loci (mean number of alleles per locus = 2.80; mean expected heterozygosity = 0.36) with no evidence of individual loci deviating significantly from Hardy-Weinberg equilibrium. Marker independence was confirmed with tests for linkage disequilibrium, and analyses indicated no evidence of null alleles across loci. Individuals from two additional sites (Crawford River, Victoria; Ewens Ponds Conservation Park, South Australia) were genotyped at all 10 loci and a preliminary investigation of genetic diversity and population structure was undertaken. Analyses indicate high levels of genetic differentiation among sample locations (F ST = 0.49), while the Ewens Ponds population is genetically homogeneous, indicating a likely small founder group and ongoing inbreeding. Management actions will be needed to restore genetic diversity in this and possibly other at risk populations. These markers will provide a valuable resource for future population genetic assessments so that an effective framework can be developed for implementing conservation strategies for E. bispinosus.

Screening and analyzing genes associated with Amur tiger placental development.

PubMed

Li, Q; Lu, T F; Liu, D; Hu, P F; Sun, B; Ma, J Z; Wang, W J; Wang, K F; Zhang, W X; Chen, J; Guan, W J; Ma, Y H; Zhang, M H

2014-09-26

The Amur tiger is a unique endangered species in the world, and thus, protection of its genetic resources is extremely important. In this study, an Amur tiger placenta cDNA library was constructed using the SMART cDNA Library Construction kit. A total of 508 colonies were sequenced, in which 205 (76%) genes were annotated and mapped to 74 KEGG pathways, including 29 metabolism, 29 genetic information processing, 4 environmental information processing, 7 cell motility, and 5 organismal system pathways. Additionally, PLAC8, PEG10 and IGF-II were identified after screening genes from the expressed sequence tags, and they were associated with placental development. These findings could lay the foundation for future functional genomic studies of the Amur tiger.

Microsatellites for Carpotroche brasiliensis (Flacourtiaceae), a useful species for agroforestry and ecosystem conservation.

PubMed

Bittencourt, Flora; Alves, Jackeline S; Gaiotto, Fernanda A

2015-12-01

We developed microsatellite markers for Carpotroche brasiliensis (Flacourtiaceae), a dioecious tree that is used as a food resource by midsize animals of the Brazilian fauna. We designed 30 primer pairs using next-generation sequencing and classified 25 pairs as polymorphic. Observed heterozygosity ranged from 0.5 to 1.0, and expected heterozygosity ranged from 0.418 to 0.907. The combined probability of exclusion was greater than 0.999 and the combined probability of identity was less than 0.001, indicating that these microsatellites are appropriate for investigations of genetic structure, individual identification, and paternity testing. The developed molecular tools may contribute to future studies of population genetics, answering ecological and evolutionary questions regarding efficient conservation strategies for C. brasiliensis.

Assessment of exchange of crop in view of change climate and International Treaties.

PubMed

Singh, Anil Kumar; Pedapati, Annitaa; Manibhushan

2015-01-01

To meet the UN millennium development goal of reducing the number of hungry people to half by 2015, there is utmost need to breed potentially high yielding varieties to match up the requirement along with corrective measures to bridge the gap between the potential yield and yield harvested by farmers. The scenario has changed from free access to limited access of plant genetic resources (PGR) and therefore, it is important to understand the issues in view of national and international agreements, intellectual property rights (IPR'S), climate change conditions and expanded scope of breeders and farmers rights for developed genotypes. For efficient management of PGR, developing countries need to understand the implications of PGR related IPR'S as stronger IPR'S in developed countries could have harmful effects by reduced exchange of genetic resources from developed countries. Keeping in view the existing realities every possible effort should be taken for enrichment of crop gene pool by introducing them from each and every corner of the globe. Keeping these facts in view this paper describes the priorities for introduction and exchange of important crop groups/crops along with some of their potential wild and weedy relatives and thrust has been given to generate awareness among the workers engaged in the breeders/crop improvement works. Information provided in this presentation can be utilized by prospective crop improvement works to plan to meet out the nationalfood security.

Incorporating a New Bioinformatics Component into Genetics at a Historically Black College: Outcomes and Lessons

ERIC Educational Resources Information Center

Holtzclaw, J. David; Eisen, Arri; Whitney, Erika M.; Penumetcha, Meera; Hoey, J. Joseph; Kimbro, K. Sean

2006-01-01

Many students at minority-serving institutions are underexposed to Internet resources such as the human genome project, PubMed, NCBI databases, and other Web-based technologies because of a lack of financial resources. To change this, we designed and implemented a new bioinformatics component to supplement the undergraduate Genetics course at…

Updates to the Cool Season Food Legume Genome Database: Resources for pea, lentil, faba bean and chickpea genetics, genomics and breeding

USDA-ARS?s Scientific Manuscript database

The Cool Season Food Legume Genome database (CSFL, www.coolseasonfoodlegume.org) is an online resource for genomics, genetics, and breeding research for chickpea, lentil,pea, and faba bean. The user-friendly and curated website allows for all publicly available map,marker,trait, gene,transcript, ger...

Sequencing Genetics Information: Integrating Data into Information Literacy for Undergraduate Biology Students

ERIC Educational Resources Information Center

MacMillan, Don

2010-01-01

This case study describes an information literacy lab for an undergraduate biology course that leads students through a range of resources to discover aspects of genetic information. The lab provides over 560 students per semester with the opportunity for hands-on exploration of resources in steps that simulate the pathways of higher-level…

Breeding strategies for north central tree improvement programs

Treesearch

Ronald P. Overton; Hyun Kang

1985-01-01

The rationales and concepts of long-term tree breeding are discussed and compared with those for short-term breeding. A model breeding program is reviewed which maximizes short-term genetic gain for currently important traits and provides genetic resources that can be used effectively in future short-term breeding. The resources of the north-central region are examined...

Genetic variation and gene expression across multiple tissues and developmental stages in a non-human primate

PubMed Central

Jasinska, Anna J.; Zelaya, Ivette; Service, Susan K.; Peterson, Christine B.; Cantor, Rita M.; Choi, Oi-Wa; DeYoung, Joseph; Eskin, Eleazar; Fairbanks, Lynn A.; Fears, Scott; Furterer, Allison E.; Huang, Yu S.; Ramensky, Vasily; Schmitt, Christopher A.; Svardal, Hannes; Jorgensen, Matthew J.; Kaplan, Jay R.; Villar, Diego; Aken, Bronwen L.; Flicek, Paul; Nag, Rishi; Wong, Emily S.; Blangero, John; Dyer, Thomas D.; Bogomolov, Marina; Benjamini, Yoav; Weinstock, George M.; Dewar, Ken; Sabatti, Chiara; Wilson, Richard K.; Jentsch, J. David; Warren, Wesley; Coppola, Giovanni; Woods, Roger P.; Freimer, Nelson B.

2017-01-01

By analyzing multi-tissue gene expression and genome-wide genetic variation data in samples from a vervet monkey pedigree, we generated a transcriptome resource and produced the first catalogue of expression quantitative trait loci (eQTLs) in a non-human primate model. This catalogue contains more genome-wide significant eQTLs, per sample, than comparable human resources, and reveals sex and age-related expression patterns. Findings include a master regulatory locus that likely plays a role in immune function, and a locus regulating hippocampal long non-coding RNAs (lncRNAs), whose expression correlates with hippocampal volume. This resource will facilitate genetic investigation of quantitative traits, including brain and behavioral phenotypes relevant to neuropsychiatric disorders. PMID:29083405

Development of novel SSR markers for evaluation of genetic diversity and population structure in Tribulus terrestris L. (Zygophyllaceae).

PubMed

Kaur, Kuljit; Sharma, Vikas; Singh, Vijay; Wani, Mohammad Saleem; Gupta, Raghbir Chand

2016-12-01

Tribulus terrestris L., commonly called puncture vine and gokhru, is an important member of Zygophyllaceae. The species is highly important in context to therapeutic uses and provides important active principles responsible for treatment of various diseases and also used as tonic. It is widely distributed in tropical regions of India and the world. However, status of its genetic diversity remained concealed due to lack of research work in this species. In present study, genetic diversity and structure of different populations of T. terrestris from north India was examined at molecular level using newly developed Simple Sequence Repeat (SSR) markers. In total, 20 primers produced 48 alleles in a size range of 100-500 bp with maximum (4) fragments amplified by TTMS-1, TTMS-25 and TTMS-33. Mean Polymorphism Information Content (PIC) and Marker Index (MI) were 0.368 and 1.01, respectively. Dendrogram showed three groups, one of which was purely containing accessions from Rajasthan while other two groups corresponded to Punjab and Haryana regions with intermixing of few other accessions. Analysis of molecular variance partitioned 76 % genetic variance within populations and 24 % among populations. Bayesian model based STRUCTURE analysis detected two genetic stocks for analyzed germplasm and also detected some admixed individuals. Different geographical populations of this species showed high level of genetic diversity. Results of present study can be useful in identifying diverse accessions and management of this plant resource. Moreover, the novel SSR markers developed can be utilized for various genetic analyses in this species in future.

Genetics education for health professionals: strategies and outcomes from a national initiative in the United Kingdom.

PubMed

Farndon, Peter A; Bennett, Catherine

2008-04-01

The National Health Service (NHS) National Genetics Education and Development Centre was established by the Department of Health in 2004 to help drive and co-ordinate genetics education for health professionals working outside specialist genetic services. This paper reviews the experiences and lessons learned to date. At the outset, it was clear that understanding the learning ethos, preferred delivery methods and attitudes towards genetics of different NHS healthcare groups was vital. We collected evidence by undertaking needs assessments with educators, practitioners and patients. We have determined the genetics knowledge, skills and attitudes which they said were needed and translated these into learning outcomes and workforce competences in a continuum of education. Beginning with core concepts introduced (and examined) pre-registration, the continuum continues with development of concepts post-registration as appropriate for role, leading to practical application and assessment of competences in the workplace. These are supported by a portfolio of resources which draw heavily on patient based scenarios to demonstrate to staff that genetics is relevant to their work, and to convince educators and policy makers that genetic education is likely to result in real clinical benefit. A long term educational policy, inclusive of learners, educationalists and their institutions must be evidence based, flexible and responsive to changes in workforce structure, provision of clinical services and conceptual and financial commitments to education. The engagement of national policy, regulatory and professional bodies is vital (www.geneticseducation.nhs.uk).

[Research progress of genetic engineering on medicinal plants].

PubMed

Teng, Zhong-qiu; Shen, Ye

2015-02-01

The application of genetic engineering technology in modern agriculture shows its outstanding role in dealing with food shortage. Traditional medicinal plant cultivation and collection have also faced with challenges, such as lack of resources, deterioration of environment, germplasm of recession and a series of problems. Genetic engineering can be used to improve the disease resistance, insect resistance, herbicides resistant ability of medicinal plant, also can improve the medicinal plant yield and increase the content of active substances in medicinal plants. Thus, the potent biotechnology can play an important role in protection and large area planting of medicinal plants. In the development of medicinal plant genetic engineering, the safety of transgenic medicinal plants should also be paid attention to. A set of scientific safety evaluation and judgment standard which is suitable for transgenic medicinal plants should be established based on the recognition of the particularity of medicinal plants.

Physiological breeding.

PubMed

Reynolds, Matthew; Langridge, Peter

2016-06-01

Physiological breeding crosses parents with different complex but complementary traits to achieve cumulative gene action for yield, while selecting progeny using remote sensing, possibly in combination with genomic selection. Physiological approaches have already demonstrated significant genetic gains in Australia and several developing countries of the International Wheat Improvement Network. The techniques involved (see Graphical Abstract) also provide platforms for research and refinement of breeding methodologies. Recent examples of these include screening genetic resources for novel expression of Calvin cycle enzymes, identification of common genetic bases for heat and drought adaptation, and genetic dissection of trade-offs among yield components. Such information, combined with results from physiological crosses designed to test novel trait combinations, lead to more precise breeding strategies, and feed models of genotype-by-environment interaction to help build new plant types and experimental environments for future climates. Copyright © 2016 The Author(s). Published by Elsevier Ltd.. All rights reserved.

Biological/Genetic Regulation of Physical Activity Level: Consensus from GenBioPAC.

PubMed

Lightfoot, J Timothy; DE Geus, Eco J C; Booth, Frank W; Bray, Molly S; DEN Hoed, Marcel; Kaprio, Jaakko; Kelly, Scott A; Pomp, Daniel; Saul, Michael C; Thomis, Martine A; Garland, Theodore; Bouchard, Claude

2018-04-01

Physical activity unquestionably maintains and improves health; however, physical activity levels globally are low and not rising despite all the resources devoted to this goal. Attention in both the research literature and the public policy domain has focused on social-behavioral factors; however, a growing body of literature suggests that biological determinants play a significant role in regulating physical activity levels. For instance, physical activity level, measured in various manners, has a genetic component in both humans and nonhuman animal models. This consensus article, developed as a result of an American College of Sports Medicine-sponsored round table, provides a brief review of the theoretical concepts and existing literature that supports a significant role of genetic and other biological factors in the regulation of physical activity. Future research on physical activity regulation should incorporate genetics and other biological determinants of physical activity instead of a sole reliance on social and other environmental determinants.

Environmental isolation explains Iberian genetic diversity in the highly homozygous model grass Brachypodium distachyon.

PubMed

Marques, Isabel; Shiposha, Valeriia; López-Alvarez, Diana; Manzaneda, Antonio J; Hernandez, Pilar; Olonova, Marina; Catalán, Pilar

2017-06-15

Brachypodium distachyon (Poaceae), an annual Mediterranean Aluminum (Al)-sensitive grass, is currently being used as a model species to provide new information on cereals and biofuel crops. The plant has a short life cycle and one of the smallest genomes in the grasses being well suited to experimental manipulation. Its genome has been fully sequenced and several genomic resources are being developed to elucidate key traits and gene functions. A reliable germplasm collection that reflects the natural diversity of this species is therefore needed for all these genomic resources. However, despite being a model plant, we still know very little about its genetic diversity. As a first step to overcome this gap, we used nuclear Simple Sequence Repeats (nSSR) to study the patterns of genetic diversity and population structure of B. distachyon in 14 populations sampled across the Iberian Peninsula (Spain), one of its best known areas. We found very low levels of genetic diversity, allelic number and heterozygosity in B. distachyon, congruent with a highly selfing system. Our results indicate the existence of at least three genetic clusters providing additional evidence for the existence of a significant genetic structure in the Iberian Peninsula and supporting this geographical area as an important genetic reservoir. Several hotspots of genetic diversity were detected and populations growing on basic soils were significantly more diverse than those growing in acidic soils. A partial Mantel test confirmed a statistically significant Isolation-By-Distance (IBD) among all studied populations, as well as a statistically significant Isolation-By-Environment (IBE) revealing the presence of environmental-driven isolation as one explanation for the genetic patterns found in the Iberian Peninsula. The finding of higher genetic diversity in eastern Iberian populations occurring in basic soils suggests that these populations can be better adapted than those occurring in western areas of the Iberian Peninsula where the soils are more acidic and accumulate toxic Al ions. This suggests that the western Iberian acidic soils might prevent the establishment of Al-sensitive B. distachyon populations, potentially causing the existence of more genetically depauperated individuals.

Using Genetically Engineered Animal Models in the Postgenomic Era to Understand Gene Function in Alcoholism

PubMed Central

Reilly, Matthew T.; Harris, R. Adron; Noronha, Antonio

2012-01-01

Over the last 50 years, researchers have made substantial progress in identifying genetic variations that underlie the complex phenotype of alcoholism. Not much is known, however, about how this genetic variation translates into altered biological function. Genetic animal models recapitulating specific characteristics of the human condition have helped elucidate gene function and the genetic basis of disease. In particular, major advances have come from the ability to manipulate genes through a variety of genetic technologies that provide an unprecedented capacity to determine gene function in the living organism and in alcohol-related behaviors. Even newer genetic-engineering technologies have given researchers the ability to control when and where a specific gene or mutation is activated or deleted, allowing investigators to narrow the role of the gene’s function to circumscribed neural pathways and across development. These technologies are important for all areas of neuroscience, and several public and private initiatives are making a new generation of genetic-engineering tools available to the scientific community at large. Finally, high-throughput “next-generation sequencing” technologies are set to rapidly increase knowledge of the genome, epigenome, and transcriptome, which, combined with genetically engineered mouse mutants, will enhance insight into biological function. All of these resources will provide deeper insight into the genetic basis of alcoholism. PMID:23134044

Using genetically engineered animal models in the postgenomic era to understand gene function in alcoholism.

PubMed

Reilly, Matthew T; Harris, R Adron; Noronha, Antonio

2012-01-01

Over the last 50 years, researchers have made substantial progress in identifying genetic variations that underlie the complex phenotype of alcoholism. Not much is known, however, about how this genetic variation translates into altered biological function. Genetic animal models recapitulating specific characteristics of the human condition have helped elucidate gene function and the genetic basis of disease. In particular, major advances have come from the ability to manipulate genes through a variety of genetic technologies that provide an unprecedented capacity to determine gene function in the living organism and in alcohol-related behaviors. Even newer genetic-engineering technologies have given researchers the ability to control when and where a specific gene or mutation is activated or deleted, allowing investigators to narrow the role of the gene's function to circumscribed neural pathways and across development. These technologies are important for all areas of neuroscience, and several public and private initiatives are making a new generation of genetic-engineering tools available to the scientific community at large. Finally, high-throughput "next-generation sequencing" technologies are set to rapidly increase knowledge of the genome, epigenome, and transcriptome, which, combined with genetically engineered mouse mutants, will enhance insight into biological function. All of these resources will provide deeper insight into the genetic basis of alcoholism.

Application of Genetic/Genomic Approaches to Allergic Disorders

PubMed Central

Baye, Tesfaye M.; Martin, Lisa J.; Khurana Hershey, Gurjit K.

2010-01-01

Completion of the human genome project and rapid progress in genetics and bioinformatics have enabled the development of large public databases, which include genetic and genomic data linked to clinical health data. With the massive amount of information available, clinicians and researchers have the unique opportunity to complement and integrate their daily practice with the existing resources to clarify the underlying etiology of complex phenotypes such as allergic diseases. The genome itself is now often utilized as a starting point for many studies and multiple innovative approaches have emerged applying genetic/genomic strategies to key questions in the field of allergy and immunology. There have been several successes, which have uncovered new insights into the biologic underpinnings of allergic disorders. Herein, we will provide an in depth review of genomic approaches to identifying genes and biologic networks involved in allergic diseases. We will discuss genetic and phenotypic variation, statistical approaches for gene discovery, public databases, functional genomics, clinical implications, and the challenges that remain. PMID:20638111

Survival and genetic stability of Dendranthema grandiflora Tzvelev shoot apices after cryopreservation by vitrification and encapsulation-dehydration.

PubMed

Martín, Carmen; González-Benito, M Elena

2005-12-01

The aim of this study was to compare the genetic stability of chrysanthemum (cv. Pasodoble) apices cryopreserved using two different methods: encapsulation-dehydration and vitrification. The assessment of the genetic stability was developed using RAPDs markers. Assessment of stability was evaluated in pot-cultivated mother plants (from which buds were excised for micropropagation), in shoots (leave tissue) from which apices were extracted for cryopreservation, and in shoots regenerated from cryopreserved apices 30 days after recovery and after further 3 months in culture. Throughout the process the origin of the apices (in vitro-shoot from which they were excised) was recorded. Twenty one regenerants cryopreserved by vitrification and 25 by encapsulation-dehydration were assessed. Only one cryopreserved regenerant from the encapsulation-dehydration method showed a different band pattern. These results support the necessity of monitoring the genetic stability of the regenerants obtained after cryopreservation, as this is a very useful technique for the conservation of plant genetic resources.

Development of a 63K SNP array for Gossypium and high-density mapping of intra- and inter-specific populations of cotton (G. hirsutum L.)

USDA-ARS?s Scientific Manuscript database

High-throughput genotyping arrays provide a standardized resource for crop research communities that are useful for a breadth of applications including high-density genetic mapping, genome-wide association studies (GWAS), genomic selection (GS), candidate marker and quantitative trait loci (QTL) ide...

Genetic and environmental effects in the TeQing-into-Lemont (TIL) population under flooded and alternating wet-dry conditions

USDA-ARS?s Scientific Manuscript database

Over the last decade there has been growing concern regarding sustainability of US rice production due to multi-year droughts and depletion of ground water resources. There is a need for research to develop rice varieties that are optimized for production using less irrigation water. One rice produc...

Development and Characterization of Novel SSR Markers in Carrot (Daucus Carota L.) and Their Application for Mapping and Diversity Analysis in Apiaceae

USDA-ARS?s Scientific Manuscript database

Genomic resources in carrot and other Apiaceae are relatively underdeveloped. The availability of a large set of pcr-based codominant markers, such as simple sequence repeats (SSR), would allow integration of the different carrot genetic maps constructed to date (mainly using anonymous dominant mark...

Fleet DNA Brings Fleet Data to Life, Informs R&D | News | NREL

Science.gov Websites

over 11.5 million miles of real-world data from more than 1,700 medium- and heavy-duty vehicles -cycle summaries and visualizations similar to real-world genetics, helping users understand the broad real-world data is a national resource that enables insight critical to the successful development of

A Survey of U.S.-Based Efforts To Research and Conserve Biological Diversity in Developing Countries.

ERIC Educational Resources Information Center

Abramovitz, Janet N.

The increasing loss of biological diversity, resulting from the loss of genetic diversity, the extinction of species, and the destruction of ecosystems, constitutes a crisis of global proportions. The resources being committed to its resolution are relatively small. This document summarizes a survey of U.S.-based organizations involved in…

Evaluation of Genetic Diversity and Development of a Core Collection of Wild Rice (Oryza rufipogon Griff.) Populations in China

PubMed Central

Bai, Lin; Lu, Zhenzhen; Chen, Yuhong; Jiang, Lan; Diao, Mengyang; Liu, Xiangdong; Lu, Yonggen

2015-01-01

Common wild rice (Oryza rufipogon Griff.), the progenitor of Asian cultivated rice (O. sativa L.), is endangered due to habitat loss. The objectives of this research were to evaluate the genetic diversity of wild rice species in isolated populations and to develop a core collection of representative genotypes for ex situ conservation. We collected 885 wild rice accessions from eight geographically distinct regions and transplanted these accessions in a protected conservation garden over a period of almost two decades. We evaluated these accessions for 13 morphological or phenological traits and genotyped them for 36 DNA markers evenly distributed on the 12 chromosomes. The coefficient of variation of quantitative traits was 0.56 and ranged from 0.37 to 1.06. SSR markers detected 206 different alleles with an average of 6 alleles per locus. The mean polymorphism information content (PIC) was 0.64 in all populations, indicating that the marker loci have a high level of polymorphism and genetic diversity in all populations. Phylogenetic analyses based on morphological and molecular data revealed remarkable differences in the genetic diversity of common wild rice populations. The results showed that the Zengcheng, Gaozhou, and Suixi populations possess higher levels of genetic diversity, whereas the Huilai and Boluo populations have lower levels of genetic diversity than do the other populations. Based on their genetic distance, 130 accessions were selected as a core collection that retained over 90% of the alleles at the 36 marker loci. This genetically diverse core collection will be a useful resource for genomic studies of rice and for initiatives aimed at developing rice with improved agronomic traits. PMID:26720755

Evaluation of Genetic Diversity and Development of a Core Collection of Wild Rice (Oryza rufipogon Griff.) Populations in China.

PubMed

Liu, Wen; Shahid, Muhammad Qasim; Bai, Lin; Lu, Zhenzhen; Chen, Yuhong; Jiang, Lan; Diao, Mengyang; Liu, Xiangdong; Lu, Yonggen

2015-01-01

Common wild rice (Oryza rufipogon Griff.), the progenitor of Asian cultivated rice (O. sativa L.), is endangered due to habitat loss. The objectives of this research were to evaluate the genetic diversity of wild rice species in isolated populations and to develop a core collection of representative genotypes for ex situ conservation. We collected 885 wild rice accessions from eight geographically distinct regions and transplanted these accessions in a protected conservation garden over a period of almost two decades. We evaluated these accessions for 13 morphological or phenological traits and genotyped them for 36 DNA markers evenly distributed on the 12 chromosomes. The coefficient of variation of quantitative traits was 0.56 and ranged from 0.37 to 1.06. SSR markers detected 206 different alleles with an average of 6 alleles per locus. The mean polymorphism information content (PIC) was 0.64 in all populations, indicating that the marker loci have a high level of polymorphism and genetic diversity in all populations. Phylogenetic analyses based on morphological and molecular data revealed remarkable differences in the genetic diversity of common wild rice populations. The results showed that the Zengcheng, Gaozhou, and Suixi populations possess higher levels of genetic diversity, whereas the Huilai and Boluo populations have lower levels of genetic diversity than do the other populations. Based on their genetic distance, 130 accessions were selected as a core collection that retained over 90% of the alleles at the 36 marker loci. This genetically diverse core collection will be a useful resource for genomic studies of rice and for initiatives aimed at developing rice with improved agronomic traits.

BIOREL: the benchmark resource to estimate the relevance of the gene networks.

PubMed

Antonov, Alexey V; Mewes, Hans W

2006-02-06

The progress of high-throughput methodologies in functional genomics has lead to the development of statistical procedures to infer gene networks from various types of high-throughput data. However, due to the lack of common standards, the biological significance of the results of the different studies is hard to compare. To overcome this problem we propose a benchmark procedure and have developed a web resource (BIOREL), which is useful for estimating the biological relevance of any genetic network by integrating different sources of biological information. The associations of each gene from the network are classified as biologically relevant or not. The proportion of genes in the network classified as "relevant" is used as the overall network relevance score. Employing synthetic data we demonstrated that such a score ranks the networks fairly in respect to the relevance level. Using BIOREL as the benchmark resource we compared the quality of experimental and theoretically predicted protein interaction data.

Explore the impacts of river flow and quality on biodiversity for water resources management by AI techniques

NASA Astrophysics Data System (ADS)

Chang, Fi-John; Tsai Tsai, Wen-Ping; Chang, Li-Chiu

2016-04-01

Water resources development is very challenging in Taiwan due to her diverse geographic environment and climatic conditions. To pursue sustainable water resources development, rationality and integrity is essential for water resources planning. River water quality and flow regimes are closely related to each other and affect river ecosystems simultaneously. This study aims to explore the complex impacts of water quality and flow regimes on fish community in order to comprehend the situations of the eco-hydrological system in the Danshui River of northern Taiwan. To make an effective and comprehensive strategy for sustainable water resources management, this study first models fish diversity through implementing a hybrid artificial neural network (ANN) based on long-term observational heterogeneity data of water quality, stream flow and fish species in the river. Then we use stream flow to estimate the loss of dissolved oxygen based on back-propagation neural networks (BPNNs). Finally, the non-dominated sorting genetic algorithm II (NSGA-II) is established for river flow management over the Shihmen Reservoir which is the main reservoir in this study area. In addition to satisfying the water demands of human beings and ecosystems, we also consider water quality for river flow management. The ecosystem requirement takes the form of maximizing fish diversity, which can be estimated by the hybrid ANN. The human requirement is to provide a higher satisfaction degree of water supply while the water quality requirement is to reduce the loss of dissolved oxygen in the river among flow stations. The results demonstrate that the proposed methodology can offer diversified alternative strategies for reservoir operation and improve reservoir operation strategies for producing downstream flows that could better meet both human and ecosystem needs as well as maintain river water quality. Keywords: Artificial intelligence (AI), Artificial neural networks (ANNs), Non-dominated sorting genetic algorithm II (NSGA-II), Sustainable water resources management, Flow regime, River ecosystem.

A gene-based SNP resource and linkage map for the copepod Tigriopus californicus

PubMed Central

2011-01-01

Background As yet, few genomic resources have been developed in crustaceans. This lack is particularly evident in Copepoda, given the extraordinary numerical abundance, and taxonomic and ecological diversity of this group. Tigriopus californicus is ideally suited to serve as a genetic model copepod and has been the subject of extensive work in environmental stress and reproductive isolation. Accordingly, we set out to develop a broadly-useful panel of genetic markers and to construct a linkage map dense enough for quantitative trait locus detection in an interval mapping framework for T. californicus--a first for copepods. Results One hundred and ninety Single Nucleotide Polymorphisms (SNPs) were used to genotype our mapping population of 250 F2 larvae. We were able to construct a linkage map with an average intermarker distance of 1.8 cM, and a maximum intermarker distance of 10.3 cM. All markers were assembled into linkage groups, and the 12 linkage groups corresponded to the 12 known chromosomes of T. californicus. We estimate a total genome size of 401.0 cM, and a total coverage of 73.7%. Seventy five percent of the mapped markers were detected in 9 additional populations of T. californicus. Of available model arthropod genomes, we were able to show more colocalized pairs of homologues between T. californicus and the honeybee Apis mellifera, than expected by chance, suggesting preserved macrosynteny between Hymenoptera and Copepoda. Conclusions Our study provides an abundance of linked markers spanning all chromosomes. Many of these markers are also found in multiple populations of T. californicus, and in two other species in the genus. The genomic resource we have developed will enable mapping throughout the geographical range of this species and in closely related species. This linkage map will facilitate genome sequencing, mapping and assembly in an ecologically and taxonomically interesting group for which genomic resources are currently under development. PMID:22103327

Breeding-assisted genomics.

PubMed

Poland, Jesse

2015-04-01

The revolution of inexpensive sequencing has ushered in an unprecedented age of genomics. The promise of using this technology to accelerate plant breeding is being realized with a vision of genomics-assisted breeding that will lead to rapid genetic gain for expensive and difficult traits. The reality is now that robust phenotypic data is an increasing limiting resource to complement the current wealth of genomic information. While genomics has been hailed as the discipline to fundamentally change the scope of plant breeding, a more symbiotic relationship is likely to emerge. In the context of developing and evaluating large populations needed for functional genomics, none excel in this area more than plant breeders. While genetic studies have long relied on dedicated, well-structured populations, the resources dedicated to these populations in the context of readily available, inexpensive genotyping is making this philosophy less tractable relative to directly focusing functional genomics on material in breeding programs. Through shifting effort for basic genomic studies from dedicated structured populations, to capturing the entire scope of genetic determinants in breeding lines, we can move towards not only furthering our understanding of functional genomics in plants, but also rapidly improving crops for increased food security, availability and nutrition. Copyright © 2015 Elsevier Ltd. All rights reserved.

Development of 23 novel polymorphic EST-SSR markers for the endangered relict conifer Metasequoia glyptostroboides.

PubMed

Jin, Yuqing; Bi, Quanxin; Guan, Wenbin; Mao, Jian-Feng

2015-09-01

Metasequoia glyptostroboides is an endangered relict conifer species endemic to China. In this study, expressed sequence tag-simple sequence repeat (EST-SSR) markers were developed using transcriptome mining for future genetic and functional studies. We collected 97,565 unigene sequences generated by 454 pyrosequencing. A bioinformatics analysis identified 2087 unique and putative microsatellites, from which 96 novel microsatellite markers were developed. Fifty-three of the 96 primer sets successfully amplified clear fragments of the expected sizes; 23 of those loci were polymorphic. The number of alleles per locus ranged from two to eight, with an average of three, and the observed and expected heterozygosity values ranged from 0 to 1.0 and 0.117 to 0.813, respectively. These microsatellite loci will enrich the genetic resources to develop functional studies and conservation strategies for this endangered relict species.

Development of 23 novel polymorphic EST-SSR markers for the endangered relict conifer Metasequoia glyptostroboides1

PubMed Central

Jin, Yuqing; Bi, Quanxin; Guan, Wenbin; Mao, Jian-Feng

2015-01-01

Premise of the study: Metasequoia glyptostroboides is an endangered relict conifer species endemic to China. In this study, expressed sequence tag–simple sequence repeat (EST-SSR) markers were developed using transcriptome mining for future genetic and functional studies. Methods and Results: We collected 97,565 unigene sequences generated by 454 pyrosequencing. A bioinformatics analysis identified 2087 unique and putative microsatellites, from which 96 novel microsatellite markers were developed. Fifty-three of the 96 primer sets successfully amplified clear fragments of the expected sizes; 23 of those loci were polymorphic. The number of alleles per locus ranged from two to eight, with an average of three, and the observed and expected heterozygosity values ranged from 0 to 1.0 and 0.117 to 0.813, respectively. Conclusions: These microsatellite loci will enrich the genetic resources to develop functional studies and conservation strategies for this endangered relict species. PMID:26421250

Characterization of the Newly Developed Soybean Cultivar DT2008 in Relation to the Model Variety W82 Reveals a New Genetic Resource for Comparative and Functional Genomics for Improved Drought Tolerance

PubMed Central

Ha, Chien Van; Le, Dung Tien; Nishiyama, Rie; Watanabe, Yasuko; Tran, Uyen Thi; Dong, Nguyen Van; Tran, Lam-Son Phan

2013-01-01

Soybean (Glycine max) productivity is adversely affected by drought stress worldwide, including Vietnam. In the last few years, we have made a great effort in the development of drought-tolerant soybean cultivars by breeding and/or radiation-induced mutagenesis. One of the newly developed cultivars, the DT2008, showed enhanced drought tolerance and stable yield in the field conditions. The purpose of this study was to compare the drought-tolerant phenotype of DT2008 and Williams 82 (W82) by assessing their water loss and growth rate under dehydration and/or drought stress conditions as a means to provide genetic resources for further comparative and functional genomics. We found that DT2008 had reduced water loss under both dehydration and drought stresses in comparison with W82. The examination of root and shoot growths of DT2008 and W82 under both normal and drought conditions indicated that DT2008 maintains a better shoot and root growth rates than W82 under both two growth conditions. These results together suggest that DT2008 has better drought tolerance degree than W82. Our results open the way for further comparison of DT2008 and W82 at molecular levels by advanced omic approaches to identify mutation(s) involved in the enhancement of drought tolerance of DT2008, contributing to our understanding of drought tolerance mechanisms in soybean. Mutation(s) identified are potential candidates for genetic engineering of elite soybean varieties to improve drought tolerance and biomass. PMID:23509774

Genetic resources for maize cell wall biology.

PubMed

Penning, Bryan W; Hunter, Charles T; Tayengwa, Reuben; Eveland, Andrea L; Dugard, Christopher K; Olek, Anna T; Vermerris, Wilfred; Koch, Karen E; McCarty, Donald R; Davis, Mark F; Thomas, Steven R; McCann, Maureen C; Carpita, Nicholas C

2009-12-01

Grass species represent a major source of food, feed, and fiber crops and potential feedstocks for biofuel production. Most of the biomass is contributed by cell walls that are distinct in composition from all other flowering plants. Identifying cell wall-related genes and their functions underpins a fundamental understanding of growth and development in these species. Toward this goal, we are building a knowledge base of the maize (Zea mays) genes involved in cell wall biology, their expression profiles, and the phenotypic consequences of mutation. Over 750 maize genes were annotated and assembled into gene families predicted to function in cell wall biogenesis. Comparative genomics of maize, rice (Oryza sativa), and Arabidopsis (Arabidopsis thaliana) sequences reveal differences in gene family structure between grass species and a reference eudicot species. Analysis of transcript profile data for cell wall genes in developing maize ovaries revealed that expression within families differed by up to 100-fold. When transcriptional analyses of developing ovaries before pollination from Arabidopsis, rice, and maize were contrasted, distinct sets of cell wall genes were expressed in grasses. These differences in gene family structure and expression between Arabidopsis and the grasses underscore the requirement for a grass-specific genetic model for functional analyses. A UniformMu population proved to be an important resource in both forward- and reverse-genetics approaches to identify hundreds of mutants in cell wall genes. A forward screen of field-grown lines by near-infrared spectroscopic screen of mature leaves yielded several dozen lines with heritable spectroscopic phenotypes. Pyrolysis-molecular beam mass spectrometry confirmed that several nir mutants had altered carbohydrate-lignin compositions.

Designing and implementing sample and data collection for an international genetics study: the Type 1 Diabetes Genetics Consortium (T1DGC).

PubMed

Hilner, Joan E; Perdue, Letitia H; Sides, Elizabeth G; Pierce, June J; Wägner, Ana M; Aldrich, Alan; Loth, Amanda; Albret, Lotte; Wagenknecht, Lynne E; Nierras, Concepcion; Akolkar, Beena

2010-01-01

The Type 1 Diabetes Genetics Consortium (T1DGC) is an international project whose primary aims are to: (a) discover genes that modify type 1 diabetes risk; and (b) expand upon the existing genetic resources for type 1 diabetes research. The initial goal was to collect 2500 affected sibling pair (ASP) families worldwide. T1DGC was organized into four regional networks (Asia-Pacific, Europe, North America, and the United Kingdom) and a Coordinating Center. A Steering Committee, with representatives from each network, the Coordinating Center, and the funding organizations, was responsible for T1DGC operations. The Coordinating Center, with regional network representatives, developed study documents and data systems. Each network established laboratories for: DNA extraction and cell line production; human leukocyte antigen genotyping; and autoantibody measurement. Samples were tracked from the point of collection, processed at network laboratories and stored for deposit at National Institute for Diabetes and Digestive and Kidney Diseases (NIDDK) Central Repositories. Phenotypic data were collected and entered into the study database maintained by the Coordinating Center. T1DGC achieved its original ASP recruitment goal. In response to research design changes, the T1DGC infrastructure also recruited trios, cases, and controls. Results of genetic analyses have identified many novel regions that affect susceptibility to type 1 diabetes. T1DGC created a resource of data and samples that is accessible to the research community. Participation in T1DGC was declined by some countries due to study requirements for the processing of samples at network laboratories and/or final deposition of samples in NIDDK Central Repositories. Re-contact of participants was not included in informed consent templates, preventing collection of additional samples for functional studies. T1DGC implemented a distributed, regional network structure to reach ASP recruitment targets. The infrastructure proved robust and flexible enough to accommodate additional recruitment. T1DGC has established significant resources that provide a basis for future discovery in the study of type 1 diabetes genetics.

Use of big data in drug development for precision medicine

PubMed Central

Kim, Rosa S.; Goossens, Nicolas; Hoshida, Yujin

2016-01-01

Summary Drug development has been a costly and lengthy process with an extremely low success rate and lack of consideration of individual diversity in drug response and toxicity. Over the past decade, an alternative “big data” approach has been expanding at an unprecedented pace based on the development of electronic databases of chemical substances, disease gene/protein targets, functional readouts, and clinical information covering inter-individual genetic variations and toxicities. This paradigm shift has enabled systematic, high-throughput, and accelerated identification of novel drugs or repurposed indications of existing drugs for pathogenic molecular aberrations specifically present in each individual patient. The exploding interest from the information technology and direct-to-consumer genetic testing industries has been further facilitating the use of big data to achieve personalized Precision Medicine. Here we overview currently available resources and discuss future prospects. PMID:27430024

Engineering Large Animal Species to Model Human Diseases.

PubMed

Rogers, Christopher S

2016-07-01

Animal models are an important resource for studying human diseases. Genetically engineered mice are the most commonly used species and have made significant contributions to our understanding of basic biology, disease mechanisms, and drug development. However, they often fail to recreate important aspects of human diseases and thus can have limited utility as translational research tools. Developing disease models in species more similar to humans may provide a better setting in which to study disease pathogenesis and test new treatments. This unit provides an overview of the history of genetically engineered large animals and the techniques that have made their development possible. Factors to consider when planning a large animal model, including choice of species, type of modification and methodology, characterization, production methods, and regulatory compliance, are also covered. © 2016 by John Wiley & Sons, Inc. Copyright © 2016 John Wiley & Sons, Inc.

Transcriptomic Profiling of Fruit Development in Black Raspberry Rubus coreanus

PubMed Central

Hu, Yaodong

2018-01-01

The wild Rubus species R. coreanus, which is widely distributed in southwest China, shows great promise as a genetic resource for breeding. One of its outstanding properties is adaptation to high temperature and humidity. To facilitate its use in selection and breeding programs, we assembled de novo 179,738,287 R. coreanus reads (125 bp in length) generated by RNA sequencing from fruits at three representative developmental stages. We also used the recently released draft genome of R. occidentalis to perform reference-guided assembly. We inferred a final 95,845-transcript reference for R. coreanus. Of these genetic resources, 66,597 (69.5%) were annotated. Based on these results, we carried out a comprehensive analysis of differentially expressed genes. Flavonoid biosynthesis, phenylpropanoid biosynthesis, plant hormone signal transduction, and cutin, suberin, and wax biosynthesis pathways were significantly enriched throughout the ripening process. We identified 23 transcripts involved in the flavonoid biosynthesis pathway whose expression perfectly paralleled changes in the metabolites. Additionally, we identified 119 nucleotide-binding site leucine-rich repeat (NBS-LRR) protein-coding genes, involved in pathogen resistance, of which 74 were in the completely conserved domain. These results provide, for the first time, genome-wide genetic information for understanding developmental regulation of R. coreanus fruits. They have the potential for use in breeding through functional genetic approaches in the near future. PMID:29805970

dbWGFP: a database and web server of human whole-genome single nucleotide variants and their functional predictions.

PubMed

Wu, Jiaxin; Wu, Mengmeng; Li, Lianshuo; Liu, Zhuo; Zeng, Wanwen; Jiang, Rui

2016-01-01

The recent advancement of the next generation sequencing technology has enabled the fast and low-cost detection of all genetic variants spreading across the entire human genome, making the application of whole-genome sequencing a tendency in the study of disease-causing genetic variants. Nevertheless, there still lacks a repository that collects predictions of functionally damaging effects of human genetic variants, though it has been well recognized that such predictions play a central role in the analysis of whole-genome sequencing data. To fill this gap, we developed a database named dbWGFP (a database and web server of human whole-genome single nucleotide variants and their functional predictions) that contains functional predictions and annotations of nearly 8.58 billion possible human whole-genome single nucleotide variants. Specifically, this database integrates 48 functional predictions calculated by 17 popular computational methods and 44 valuable annotations obtained from various data sources. Standalone software, user-friendly query services and free downloads of this database are available at http://bioinfo.au.tsinghua.edu.cn/dbwgfp. dbWGFP provides a valuable resource for the analysis of whole-genome sequencing, exome sequencing and SNP array data, thereby complementing existing data sources and computational resources in deciphering genetic bases of human inherited diseases. © The Author(s) 2016. Published by Oxford University Press.

Whole genome sequences in pulse crops: a global community resource to expedite translational genomics and knowledge-based crop improvement.

PubMed

Bohra, Abhishek; Singh, Narendra P

2015-08-01

Unprecedented developments in legume genomics over the last decade have resulted in the acquisition of a wide range of modern genomic resources to underpin genetic improvement of grain legumes. The genome enabled insights direct investigators in various ways that primarily include unearthing novel structural variations, retrieving the lost genetic diversity, introducing novel/exotic alleles from wider gene pools, finely resolving the complex quantitative traits and so forth. To this end, ready availability of cost-efficient and high-density genotyping assays allows genome wide prediction to be increasingly recognized as the key selection criterion in crop breeding. Further, the high-dimensional measurements of agronomically significant phenotypes obtained by using new-generation screening techniques will empower reference based resequencing as well as allele mining and trait mapping methods to comprehensively associate genome diversity with the phenome scale variation. Besides stimulating the forward genetic systems, accessibility to precisely delineated genomic segments reveals novel candidates for reverse genetic techniques like targeted genome editing. The shifting paradigm in plant genomics in turn necessitates optimization of crop breeding strategies to enable the most efficient integration of advanced omics knowledge and tools. We anticipate that the crop improvement schemes will be bolstered remarkably with rational deployment of these genome-guided approaches, ultimately resulting in expanded plant breeding capacities and improved crop performance.

Convergence between biological, behavioural and genetic determinants of obesity.

PubMed

Ghosh, Sujoy; Bouchard, Claude

2017-12-01

Multiple biological, behavioural and genetic determinants or correlates of obesity have been identified to date. Genome-wide association studies (GWAS) have contributed to the identification of more than 100 obesity-associated genetic variants, but their roles in causal processes leading to obesity remain largely unknown. Most variants are likely to have tissue-specific regulatory roles through joint contributions to biological pathways and networks, through changes in gene expression that influence quantitative traits, or through the regulation of the epigenome. The recent availability of large-scale functional genomics resources provides an opportunity to re-examine obesity GWAS data to begin elucidating the function of genetic variants. Interrogation of knockout mouse phenotype resources provides a further avenue to test for evidence of convergence between genetic variation and biological or behavioural determinants of obesity.

Genetic evaluation of the breeding population of a valuable reforestation conifer Platycladus orientalis (Cupressaceae)

NASA Astrophysics Data System (ADS)

Jin, Yuqing; Ma, Yongpeng; Wang, Shun; Hu, Xian-Ge; Huang, Li-Sha; Li, Yue; Wang, Xiao-Ru; Mao, Jian-Feng

2016-10-01

Platycladus orientalis, a widespread conifer with long lifespan and significant adaptability. It is much used in reforestation in north China and commonly planted in central Asia. With the increasing demand for plantation forest in central to north China, breeding programs are progressively established for this species. Efficient use of breeding resources requires good understanding of the genetic value of the founder breeding materials. This study investigated the distribution of genetic variation in 192 elite trees collected for the breeding program for the central range of the species. We developed first set of 27 polymorphic EST-derived SSR loci for the species from transcriptome/genome data. After examination of amplification quality, 10 loci were used to evaluate the genetic variation in the breeding population. We found moderate genetic diversity (average He = 0.348) and low population differentiation (Fst = 0.011). Extensive admixture and no significant geographic population structure characterized this set of collections. Our analyses of the diversity and population structure are important steps toward a long-term sustainable deployment of the species and provide valuable genetic information for conservation and breeding applications.

Genetic analysis of Apuleia leiocarpa as revealed by random amplified polymorphic DNA markers: prospects for population genetic studies.

PubMed

Lencina, K H; Konzen, E R; Tsai, S M; Bisognin, D A

2016-12-19

Apuleia leiocarpa (Vogel) J.F. MacBride is a hardwood species native to South America, which is at serious risk of extinction. Therefore, it is of prime importance to examine the genetic diversity of this species, information required for developing conservation, sustainable management, and breeding strategies. Although scarcely used in recent years, random amplified polymorphic DNA markers are useful resources for the analysis of genetic diversity and structure of tree species. This study represents the first genetic analysis based on DNA markers in A. leiocarpa that aimed to investigate the levels of polymorphism and to select markers for the precise characterization of its genetic structure. We adapted the original DNA extraction protocol based on cetyltrimethyl ammonium bromide, and describe a simple procedure that can be used to obtain high-quality samples from leaf tissues of this tree. Eighteen primers were selected, revealing 92 bands, from which 75 were polymorphic and 61 were sufficient to represent the overall genetic structure of the population without compromising the precision of the analysis. Some fragments were conserved among individuals, which can be sequenced and used to analyze nucleotide diversity parameters through a wider set of A. leiocarpa individuals and populations. The individuals were separated into 11 distinct groups with variable levels of genetic diversity, which is important for selecting desirable genotypes and for the development of a conservation and sustainable management program. Our results are of prime importance for further investigations concerning the genetic characterization of this important, but vulnerable species.

First complete female mitochondrial genome in four bivalve species genus Donax and their phylogenetic relationships within the Veneroida order

PubMed Central

Nantón, Ana; Ruiz-Ruano, Francisco J.; Camacho, Juan Pedro M.; Méndez, Josefina

2017-01-01

Background Four species of the genus Donax (D. semistriatus, D. trunculus, D. variegatus and D. vittatus) are common on Iberian Peninsula coasts. Nevertheless, despite their economic importance and overexploitation, scarce genetic resources are available. In this work, we newly determined the complete mitochondrial genomes of these four representatives of the family Donacidae, with the aim of contributing to unveil phylogenetic relationships within the Veneroida order, and of developing genetic markers being useful in wedge clam identification and authentication, and aquaculture stock management. Principal findings The complete female mitochondrial genomes of the four species vary in size from 17,044 to 17,365 bp, and encode 13 protein-coding genes (including the atp8 gene), 2 rRNAs and 22 tRNAs, all located on the same strand. A long non-coding region was identified in each of the four Donax species between cob and cox2 genes, presumably corresponding to the Control Region. The Bayesian and Maximum Likelihood phylogenetic analysis of the Veneroida order indicate that all four species of Donax form a single clade as a sister group of other bivalves within the Tellinoidea superfamily. However, although Tellinoidea is actually monophyletic, none of its families are monophyletic. Conclusions Sequencing of complete mitochondrial genomes provides highly valuable information to establish the phylogenetic relationships within the Veneroida order. Furthermore, we provide here significant genetic resources for further research and conservation of this commercially important fishing resource. PMID:28886105

Cancer Genetics Overview (PDQ®)—Health Professional Version

Cancer.gov

Expert-reviewed information summary in which the features of hereditary cancer and the structure and content of other PDQ cancer genetics summaries are described. The summary also contains an extensive list of genetics resources available online.

Genetics Home Reference: cystic fibrosis

MedlinePlus

... Foundation) Genetic Testing (1 link) Genetic Testing Registry: Cystic fibrosis Other Diagnosis and Management Resources (5 links) American Society for Reproductive Medicine: Male Infertility Baby's First Test GeneReview: Cystic Fibrosis and Congenital Absence of the Vas Deferens Genomics ...

Rice diversity panels available through the genetic stocks oryza collection

USDA-ARS?s Scientific Manuscript database

The Genetic Stocks Oryza (GSOR) Collection was established in 2004 at the USDA-ARS, Dale Bumpers National Rice Research Center (DBNRRC) located in Stuttgart, AR. The mission of GSOR is to provide unique genetic resources to the rice research community for genetic and genomics related research. GSOR ...

Genetic diversity of water use efficiency in Jerusalem artichoke (Helianthus tuberosus L.) germplasm

USDA-ARS?s Scientific Manuscript database

Genetic diversity in crop germplasm is an important resource for crop improvement, but information on genetic diversity is rare for Jerusalem artichoke, especially for traits related to water use efficiency. The objectives of this study were to investigate genetic variations for water use and water...

Canadian Open Genetics Repository (COGR): a unified clinical genomics database as a community resource for standardising and sharing genetic interpretations.

PubMed

Lerner-Ellis, Jordan; Wang, Marina; White, Shana; Lebo, Matthew S

2015-07-01

The Canadian Open Genetics Repository is a collaborative effort for the collection, storage, sharing and robust analysis of variants reported by medical diagnostics laboratories across Canada. As clinical laboratories adopt modern genomics technologies, the need for this type of collaborative framework is increasingly important. A survey to assess existing protocols for variant classification and reporting was delivered to clinical genetics laboratories across Canada. Based on feedback from this survey, a variant assessment tool was made available to all laboratories. Each participating laboratory was provided with an instance of GeneInsight, a software featuring versioning and approval processes for variant assessments and interpretations and allowing for variant data to be shared between instances. Guidelines were established for sharing data among clinical laboratories and in the final outreach phase, data will be made readily available to patient advocacy groups for general use. The survey demonstrated the need for improved standardisation and data sharing across the country. A variant assessment template was made available to the community to aid with standardisation. Instances of the GeneInsight tool were provided to clinical diagnostic laboratories across Canada for the purpose of uploading, transferring, accessing and sharing variant data. As an ongoing endeavour and a permanent resource, the Canadian Open Genetics Repository aims to serve as a focal point for the collaboration of Canadian laboratories with other countries in the development of tools that take full advantage of laboratory data in diagnosing, managing and treating genetic diseases. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://group.bmj.com/group/rights-licensing/permissions.

SMART – Sunflower Mutant population And Reverse genetic Tool for crop improvement

PubMed Central

2013-01-01

Background Sunflower (Helianthus annuus L.) is an important oilseed crop grown widely in various areas of the world. Classical genetic studies have been extensively undertaken for the improvement of this particular oilseed crop. Pertaining to this endeavor, we developed a “chemically induced mutated genetic resource for detecting SNP by TILLING” in sunflower to create new traits. Results To optimize the EMS mutagenesis, we first conducted a “kill curve” analysis with a range of EMS dose from 0.5% to 3%. Based on the observed germination rate, a 50% survival rate i.e. LD50, treatment with 0.6% EMS for 8 hours was chosen to generate 5,000 M2 populations, out of which, 4,763 M3 plants with fertile seed set. Phenotypic characterization of the 5,000 M2 mutagenised lines were undertaken to assess the mutagenesis quality and to identify traits of interest. In the M2 population, about 1.1% of the plants showed phenotypic variations. The sunflower TILLING platform was setup using Endo-1-nuclease as mismatch detection system coupled with an eight fold DNA pooling strategy. As proof-of-concept, we screened the M2 population for induced mutations in two genes related to fatty acid biosynthesis, FatA an acyl-ACP thioesterase and SAD the stearoyl-ACP desaturase and identified a total of 26 mutations. Conclusion Based on the TILLING of FatA and SAD genes, we calculated the overall mutation rate to one mutation every 480 kb, similar to other report for this crop so far. As sunflower is a plant model for seed oil biosynthesis, we anticipate that the developed genetic resource will be a useful tool to identify novel traits for sunflower crop improvement. PMID:23496999

A Single Transcriptome of a Green Toad (Bufo viridis) Yields Candidate Genes for Sex Determination and -Differentiation and Non-Anonymous Population Genetic Markers

PubMed Central

Gerchen, Jörn F.; Reichert, Samuel J.; Röhr, Johannes T.; Dieterich, Christoph; Kloas, Werner

2016-01-01

Large genome size, including immense repetitive and non-coding fractions, still present challenges for capacity, bioinformatics and thus affordability of whole genome sequencing in most amphibians. Here, we test the performance of a single transcriptome to understand whether it can provide a cost-efficient resource for species with large unknown genomes. Using RNA from six different tissues from a single Palearctic green toad (Bufo viridis) specimen and Hiseq2000, we obtained 22,5 Mio reads and publish >100,000 unigene sequences. To evaluate efficacy and quality, we first use this data to identify green toad specific candidate genes, known from other vertebrates for their role in sex determination and differentiation. Of a list of 37 genes, the transcriptome yielded 32 (87%), many of which providing the first such data for this non-model anuran species. However, for many of these genes, only fragments could be retrieved. In order to allow also applications to population genetics, we further used the transcriptome for the targeted development of 21 non-anonymous microsatellites and tested them in genetic families and backcrosses. Eleven markers were specifically developed to be located on the B. viridis sex chromosomes; for eight markers we can indeed demonstrate sex-specific transmission in genetic families. Depending on phylogenetic distance, several markers, which are sex-linked in green toads, show high cross-amplification success across the anuran phylogeny, involving nine systematic anuran families. Our data support the view that single transcriptome sequencing (based on multiple tissues) provides a reliable genomic resource and cost-efficient method for non-model amphibian species with large genome size and, despite limitations, should be considered as long as genome sequencing remains unaffordable for most species. PMID:27232626

Valuation of crop genetic resources in Kaski, Nepal: farmers' willingness to pay for rice landraces conservation.

PubMed

Poudel, Diwakar; Johnsen, Fred H

2009-01-01

Crop genetic resources constitute an important aspect of biodiversity conservation, both because of their direct value to the farmers and due to their indirect global value. This study uses the contingent valuation method to document the economic value of crop genetic resources based on the farmers' willingness to pay for conservation. A total of 107 households in Kaski, Nepal were surveyed in November 2003. Their mean willingness to pay was USD 4.18 for in situ and USD 2.20 for ex situ conservation per annum. Landholding size, household size, education level, socio-economic status, sex of respondent, number of crop landraces grown, and knowledge on biodiversity influenced the willingness to pay for in situ conservation, whereas only landholding size and household size influenced the willingness to pay for ex situ conservation. The respondents were willing to contribute more for in situ than ex situ conservation because of the additional effect of direct use and direct involvement of the farmers in in situ conservation. This study supports the view that economic valuation of crop genetic resources can assist the policy makers in setting conservation priorities.

WheatGenome.info: A Resource for Wheat Genomics Resource.

PubMed

Lai, Kaitao

2016-01-01

An integrated database with a variety of Web-based systems named WheatGenome.info hosting wheat genome and genomic data has been developed to support wheat research and crop improvement. The resource includes multiple Web-based applications, which are implemented as a variety of Web-based systems. These include a GBrowse2-based wheat genome viewer with BLAST search portal, TAGdb for searching wheat second generation genome sequence data, wheat autoSNPdb, links to wheat genetic maps using CMap and CMap3D, and a wheat genome Wiki to allow interaction between diverse wheat genome sequencing activities. This portal provides links to a variety of wheat genome resources hosted at other research organizations. This integrated database aims to accelerate wheat genome research and is freely accessible via the web interface at http://www.wheatgenome.info/ .

A sustainable genetic algorithm for satellite resource allocation

NASA Technical Reports Server (NTRS)

Abbott, R. J.; Campbell, M. L.; Krenz, W. C.

1995-01-01

A hybrid genetic algorithm is used to schedule tasks for 8 satellites, which can be modelled as a robot whose task is to retrieve objects from a two dimensional field. The objective is to find a schedule that maximizes the value of objects retrieved. Typical of the real-world tasks to which this corresponds is the scheduling of ground contacts for a communications satellite. An important feature of our application is that the amount of time available for running the scheduler is not necessarily known in advance. This requires that the scheduler produce reasonably good results after a short period but that it also continue to improve its results if allowed to run for a longer period. We satisfy this requirement by developing what we call a sustainable genetic algorithm.

Management of Charcot–Marie–Tooth disease: improving long-term care with a multidisciplinary approach

PubMed Central

McCorquodale, Donald; Pucillo, Evan M; Johnson, Nicholas E

2016-01-01

Charcot–Marie–Tooth (CMT) disease is the most common inherited neuropathy and one of the most common inherited diseases in humans. The diagnosis of CMT is traditionally made by the neurologic specialist, yet the optimal management of CMT patients includes genetic counselors, physical and occupational therapists, physiatrists, orthotists, mental health providers, and community resources. Rapidly developing genetic discoveries and novel gene discovery techniques continue to add a growing number of genetic subtypes of CMT. The first large clinical natural history and therapeutic trials have added to our knowledge of each CMT subtype and revealed how CMT impacts patient quality of life. In this review, we discuss several important trends in CMT research factors that will require a collaborative multidisciplinary approach. These include the development of large multicenter patient registries, standardized clinical instruments to assess disease progression and disability, and increasing recognition and use of patient-reported outcome measures. These developments will continue to guide strategies in long-term multidisciplinary efforts to maintain quality of life and preserve functionality in CMT patients. PMID:26855581

God and Genes in the Caring Professions: Clinician and Clergy Perceptions of Religion and Genetics

PubMed Central

Bartlett, Virginia L; Johnson, Rolanda L

2013-01-01

Little is known about how care providers’ perceptions of religion and genetics affect interactions with patients/parishioners. This study investigates clinicians’ and clergy’s perceptions of and experiences with religion and genetics in their clinical and pastoral interactions. An exploratory qualitative study designed to elicit care providers’ descriptions of experiences with religion and genetics in clinical or pastoral interactions. Thirteen focus groups were conducted with members of the caring professions: physicians, nurses, and genetics counselors (clinicians), ministers and chaplains (clergy). Preliminary analysis of qualitative data is presented here. Preliminary analysis highlights four positions in professional perceptions of the relationship between science and faith. Further, differences among professional perceptions appear to influence perceptions of needed or available resources for interactions with religion and genetics. Clinicians’ and clergy’s perceptions of how religion and genetics relate are not defined solely by professional affiliation. These non-role-defined perceptions may affect clinical and pastoral interactions, especially regarding resources for patients and parishioners. PMID:19170091

Combinatorial Optimization in Project Selection Using Genetic Algorithm

NASA Astrophysics Data System (ADS)

Dewi, Sari; Sawaluddin

2018-01-01

This paper discusses the problem of project selection in the presence of two objective functions that maximize profit and minimize cost and the existence of some limitations is limited resources availability and time available so that there is need allocation of resources in each project. These resources are human resources, machine resources, raw material resources. This is treated as a consideration to not exceed the budget that has been determined. So that can be formulated mathematics for objective function (multi-objective) with boundaries that fulfilled. To assist the project selection process, a multi-objective combinatorial optimization approach is used to obtain an optimal solution for the selection of the right project. It then described a multi-objective method of genetic algorithm as one method of multi-objective combinatorial optimization approach to simplify the project selection process in a large scope.

Mining the human genome after Association for Molecular Pathology v. Myriad Genetics.

PubMed

Evans, Barbara J

2014-07-01

The Supreme Court's recent decision in Association for Molecular Pathology v. Myriad Genetics portrays the human genome as a product of nature. This frames medical genetics as an extractive industry that mines a natural resource to produce valuable goods and services. Natural resource law offers insights into problems medical geneticists can expect after this decision and suggests possible solutions. Increased competition among clinical laboratories offers various benefits but threatens to increase fragmentation of genetic data resources, potentially causing waste in the form of lost opportunities to discover the clinical significance of particular gene variants. The solution lies in addressing legal barriers to appropriate data sharing. Sustainable discovery in the field of medical genetics can best be achieved through voluntary data sharing rather than command-and-control tactics, but voluntary mechanisms must be conceived broadly to include market-based approaches as well as donative and publicly funded data commons. The recently revised Health Insurance Portability and Accountability Act Privacy Rule offers an improved--but still imperfect--framework for market-oriented data sharing. This article explores strategies for addressing the Privacy Rule's remaining defects. America is close to having a legal framework that can reward innovators, protect privacy, and promote needed data sharing to advance medical genetics.

Optimization of Land Use Suitability for Agriculture Using Integrated Geospatial Model and Genetic Algorithms

NASA Astrophysics Data System (ADS)

Mansor, S. B.; Pormanafi, S.; Mahmud, A. R. B.; Pirasteh, S.

2012-08-01

In this study, a geospatial model for land use allocation was developed from the view of simulating the biological autonomous adaptability to environment and the infrastructural preference. The model was developed based on multi-agent genetic algorithm. The model was customized to accommodate the constraint set for the study area, namely the resource saving and environmental-friendly. The model was then applied to solve the practical multi-objective spatial optimization allocation problems of land use in the core region of Menderjan Basin in Iran. The first task was to study the dominant crops and economic suitability evaluation of land. Second task was to determine the fitness function for the genetic algorithms. The third objective was to optimize the land use map using economical benefits. The results has indicated that the proposed model has much better performance for solving complex multi-objective spatial optimization allocation problems and it is a promising method for generating land use alternatives for further consideration in spatial decision-making.

Characterization and Amplification of Gene-Based Simple Sequence Repeat (SSR) Markers in Date Palm.

PubMed

Zhao, Yongli; Keremane, Manjunath; Prakash, Channapatna S; He, Guohao

2017-01-01

The paucity of molecular markers limits the application of genetic and genomic research in date palm (Phoenix dactylifera L.). Availability of expressed sequence tag (EST) sequences in date palm may provide a good resource for developing gene-based markers. This study characterizes a substantial fraction of transcriptome sequences containing simple sequence repeats (SSRs) from the EST sequences in date palm. The EST sequences studied are mainly homologous to those of Elaeis guineensis and Musa acuminata. A total of 911 gene-based SSR markers, characterized with functional annotations, have provided a useful basis not only for discovering candidate genes and understanding genetic basis of traits of interest but also for developing genetic and genomic tools for molecular research in date palm, such as diversity study, quantitative trait locus (QTL) mapping, and molecular breeding. The procedures of DNA extraction, polymerase chain reaction (PCR) amplification of these gene-based SSR markers, and gel electrophoresis of PCR products are described in this chapter.

Oceanography and life history predict contrasting genetic population structure in two Antarctic fish species.

PubMed

Young, Emma F; Belchier, Mark; Hauser, Lorenz; Horsburgh, Gavin J; Meredith, Michael P; Murphy, Eugene J; Pascoal, Sonia; Rock, Jennifer; Tysklind, Niklas; Carvalho, Gary R

2015-06-01

Understanding the key drivers of population connectivity in the marine environment is essential for the effective management of natural resources. Although several different approaches to evaluating connectivity have been used, they are rarely integrated quantitatively. Here, we use a 'seascape genetics' approach, by combining oceanographic modelling and microsatellite analyses, to understand the dominant influences on the population genetic structure of two Antarctic fishes with contrasting life histories, Champsocephalus gunnari and Notothenia rossii. The close accord between the model projections and empirical genetic structure demonstrated that passive dispersal during the planktonic early life stages is the dominant influence on patterns and extent of genetic structuring in both species. The shorter planktonic phase of C. gunnari restricts direct transport of larvae between distant populations, leading to stronger regional differentiation. By contrast, geographic distance did not affect differentiation in N. rossii, whose longer larval period promotes long-distance dispersal. Interannual variability in oceanographic flows strongly influenced the projected genetic structure, suggesting that shifts in circulation patterns due to climate change are likely to impact future genetic connectivity and opportunities for local adaptation, resilience and recovery from perturbations. Further development of realistic climate models is required to fully assess such potential impacts.

Genetics, mental illness, and complex disease: development and distribution of an interactive CD-ROM for genetic counselors. Final report for period 15 August 2000 - 31 December 2002

DOE Office of Scientific and Technical Information (OSTI.GOV)

McInerney, Joseph D.

2003-03-31

"Genetics and Major Psychiatric Disorders: A Program for Genetic Counselors" provides an introduction to psychiatric genetics, with a focus on the genetics of common complex disease, for genetics professionals. The program is available as a CD-ROM and an online educational resource. The on-line version requires a direct internet connection. Each educational module begins with an interactive case study that raises significant issues addressed in each module. In addition, case studies provided throughout the educational materials support teaching of major concepts. Incorporated throughout the content are expert video clips, video clips from individuals affected by psychiatric illness, and optional "learn more"more » materials that offer greater depth about a particular topic. The structure of the CD-ROM permits self-navigation, but we have suggested a sequence that allows materials to build upon each other. At any point in the materials, users may pause and look up terms in the glossary or review the DSM-IV criteria for selected psychiatric disorders. A detailed site map is available for those who choose to self navigate through the content.« less

Genetic diversity in the germplasm of black pepper determined by EST-SSR markers.

PubMed

Wu, B D; Fan, R; Hu, L S; Wu, H S; Hao, C Y

2016-03-18

This study aimed to assess genetic diversity in the germplasm of black pepper from around the world using SSR markers from EST. In total, 13 markers were selected and successfully amplified the target loci across the black pepper germplasm. All the EST-SSR markers showed high levels of polymorphisms with an average polymorphism information content of 0.93. The genetic similarity coefficients among all accessions ranged from 0.724 to 1.000, with an average of 0.867. These results indicated that black pepper germplasms possess a complex genetic background and high genetic diversity. Based on a cluster analysis, 148 black pepper germplasms were grouped in two major clades: the Neotropics and the Asian tropics. Peperomia pellucida was grouped separately and distantly from all other accessions. These results generally agreed with the genetic and geographic distances. However, the Asian tropics clade did not cluster according to their geographic origins. In addition, compared with the American accessions, the Asian wild accessions and cultivated accessions grouped together, indicating a close genetic relationship. This verified the origin of black pepper. The newly developed EST-SSRs are highly valuable resources for the conservation of black pepper germplasm diversity and for black pepper breeding.

Novel SSR Markers from BAC-End Sequences, DArT Arrays and a Comprehensive Genetic Map with 1,291 Marker Loci for Chickpea (Cicer arietinum L.)

PubMed Central

Nayak, Spurthi N.; Varghese, Nicy; Shah, Trushar M.; Penmetsa, R. Varma; Thirunavukkarasu, Nepolean; Gudipati, Srivani; Gaur, Pooran M.; Kulwal, Pawan L.; Upadhyaya, Hari D.; KaviKishor, Polavarapu B.; Winter, Peter; Kahl, Günter; Town, Christopher D.; Kilian, Andrzej; Cook, Douglas R.; Varshney, Rajeev K.

2011-01-01

Chickpea (Cicer arietinum L.) is the third most important cool season food legume, cultivated in arid and semi-arid regions of the world. The goal of this study was to develop novel molecular markers such as microsatellite or simple sequence repeat (SSR) markers from bacterial artificial chromosome (BAC)-end sequences (BESs) and diversity arrays technology (DArT) markers, and to construct a high-density genetic map based on recombinant inbred line (RIL) population ICC 4958 (C. arietinum)×PI 489777 (C. reticulatum). A BAC-library comprising 55,680 clones was constructed and 46,270 BESs were generated. Mining of these BESs provided 6,845 SSRs, and primer pairs were designed for 1,344 SSRs. In parallel, DArT arrays with ca. 15,000 clones were developed, and 5,397 clones were found polymorphic among 94 genotypes tested. Screening of newly developed BES-SSR markers and DArT arrays on the parental genotypes of the RIL mapping population showed polymorphism with 253 BES-SSR markers and 675 DArT markers. Segregation data obtained for these polymorphic markers and 494 markers data compiled from published reports or collaborators were used for constructing the genetic map. As a result, a comprehensive genetic map comprising 1,291 markers on eight linkage groups (LGs) spanning a total of 845.56 cM distance was developed (http://cmap.icrisat.ac.in/cmap/sm/cp/thudi/). The number of markers per linkage group ranged from 68 (LG 8) to 218 (LG 3) with an average inter-marker distance of 0.65 cM. While the developed resource of molecular markers will be useful for genetic diversity, genetic mapping and molecular breeding applications, the comprehensive genetic map with integrated BES-SSR markers will facilitate its anchoring to the physical map (under construction) to accelerate map-based cloning of genes in chickpea and comparative genome evolution studies in legumes. PMID:22102885

Generation and analysis of blueberry transcriptome sequences from leaves, developing fruit, and flower buds from cold acclimation through deacclimation.

PubMed

Rowland, Lisa J; Alkharouf, Nadim; Darwish, Omar; Ogden, Elizabeth L; Polashock, James J; Bassil, Nahla V; Main, Dorrie

2012-04-02

There has been increased consumption of blueberries in recent years fueled in part because of their many recognized health benefits. Blueberry fruit is very high in anthocyanins, which have been linked to improved night vision, prevention of macular degeneration, anti-cancer activity, and reduced risk of heart disease. Very few genomic resources have been available for blueberry, however. Further development of genomic resources like expressed sequence tags (ESTs), molecular markers, and genetic linkage maps could lead to more rapid genetic improvement. Marker-assisted selection could be used to combine traits for climatic adaptation with fruit and nutritional quality traits. Efforts to sequence the transcriptome of the commercial highbush blueberry (Vaccinium corymbosum) cultivar Bluecrop and use the sequences to identify genes associated with cold acclimation and fruit development and develop SSR markers for mapping studies are presented here. Transcriptome sequences were generated from blueberry fruit at different stages of development, flower buds at different stages of cold acclimation, and leaves by next-generation Roche 454 sequencing. Over 600,000 reads were assembled into approximately 15,000 contigs and 124,000 singletons. The assembled sequences were annotated and functionally mapped to Gene Ontology (GO) terms. Frequency of the most abundant sequences in each of the libraries was compared across all libraries to identify genes that are potentially differentially expressed during cold acclimation and fruit development. Real-time PCR was performed to confirm their differential expression patterns. Overall, 14 out of 17 of the genes examined had differential expression patterns similar to what was predicted from their reads alone. The assembled sequences were also mined for SSRs. From these sequences, 15,886 blueberry EST-SSR loci were identified. Primers were designed from 7,705 of the SSR-containing sequences with adequate flanking sequence. One hundred primer pairs were tested for amplification and polymorphism among parents of two blueberry populations currently being used for genetic linkage map construction. The tetraploid mapping population was based on a cross between the highbush cultivars Draper and Jewel (V. darrowii is also in the background of 'Jewel'). The diploid mapping population was based on a cross between an F1 hybrid of V. darrowii and diploid V. corymbosum and another diploid V. corymbosum. The overall amplification rate of the SSR primers was 68% and the polymorphism rate was 43%. These results indicate that this large collection of 454 ESTs will be a valuable resource for identifying genes that are potentially differentially expressed and play important roles in flower bud development, cold acclimation, chilling unit accumulation, and fruit development in blueberry and related species. In addition, the ESTs have already proved useful for the development of SSR and EST-PCR markers, and are currently being used for construction of genetic linkage maps in blueberry.

Generation and analysis of blueberry transcriptome sequences from leaves, developing fruit, and flower buds from cold acclimation through deacclimation

PubMed Central

2012-01-01

Background There has been increased consumption of blueberries in recent years fueled in part because of their many recognized health benefits. Blueberry fruit is very high in anthocyanins, which have been linked to improved night vision, prevention of macular degeneration, anti-cancer activity, and reduced risk of heart disease. Very few genomic resources have been available for blueberry, however. Further development of genomic resources like expressed sequence tags (ESTs), molecular markers, and genetic linkage maps could lead to more rapid genetic improvement. Marker-assisted selection could be used to combine traits for climatic adaptation with fruit and nutritional quality traits. Results Efforts to sequence the transcriptome of the commercial highbush blueberry (Vaccinium corymbosum) cultivar Bluecrop and use the sequences to identify genes associated with cold acclimation and fruit development and develop SSR markers for mapping studies are presented here. Transcriptome sequences were generated from blueberry fruit at different stages of development, flower buds at different stages of cold acclimation, and leaves by next-generation Roche 454 sequencing. Over 600,000 reads were assembled into approximately 15,000 contigs and 124,000 singletons. The assembled sequences were annotated and functionally mapped to Gene Ontology (GO) terms. Frequency of the most abundant sequences in each of the libraries was compared across all libraries to identify genes that are potentially differentially expressed during cold acclimation and fruit development. Real-time PCR was performed to confirm their differential expression patterns. Overall, 14 out of 17 of the genes examined had differential expression patterns similar to what was predicted from their reads alone. The assembled sequences were also mined for SSRs. From these sequences, 15,886 blueberry EST-SSR loci were identified. Primers were designed from 7,705 of the SSR-containing sequences with adequate flanking sequence. One hundred primer pairs were tested for amplification and polymorphism among parents of two blueberry populations currently being used for genetic linkage map construction. The tetraploid mapping population was based on a cross between the highbush cultivars Draper and Jewel (V. darrowii is also in the background of 'Jewel'). The diploid mapping population was based on a cross between an F1 hybrid of V. darrowii and diploid V. corymbosum and another diploid V. corymbosum. The overall amplification rate of the SSR primers was 68% and the polymorphism rate was 43%. Conclusions These results indicate that this large collection of 454 ESTs will be a valuable resource for identifying genes that are potentially differentially expressed and play important roles in flower bud development, cold acclimation, chilling unit accumulation, and fruit development in blueberry and related species. In addition, the ESTs have already proved useful for the development of SSR and EST-PCR markers, and are currently being used for construction of genetic linkage maps in blueberry. PMID:22471859

The Cardiff Study of all Wales and North West of England Twins (CaStANET): a longitudinal research program of child and adolescent development.

PubMed

van den Bree, Marianne B M; Rice, Frances; Fowler, Tom A; Shelton, Katherine H; Lifford, Kate J; Scourfield, Jane; Harold, Gordon T; Thapar, Anita

2007-02-01

The study of twins and their families provides a highly useful tool for disentangling the genetic and environmental origins of traits. The Cardiff Study of All Wales and North West of England Twins (CaStANET) has followed children and adolescents over time into early adulthood, assessing a wide range of aspects of behavior and psychopathology using self-, parent and teacher reports. Four main waves of data collection have taken place to date, which have provided a wealth of information on the contributions of genetic and environmental risk factors to the psychological health of young people. This article first describes the CaStANET register and subsequently presents some of the findings that have emerged from this resource, with a focus on depression and anxiety, chronic fatigue, attention-deficit/hyperactivity disorder, conduct problems and prosocial behavior. We describe in somewhat more detail the 4th wave of data collection, which has recently been completed and has provided us with extensive information on substance use and problem use as well as associated risk factors in the twins and their families, including longitudinal data on conduct problems and the relations between family members. Because of the wealth of data already collected and the opportunity for genetically informative analyses over time, CaStANET provides a valuable resource for understanding the complexities of the psychological development of young people.

iTAG Barley: A 9-12 classroom module to explore gene expression and segregation using Oregon Wolfe Barley

USDA-ARS?s Scientific Manuscript database

The Oregon Wolfe Barleys (OWBs) are a model resource for genetics research and instruction (http://barleyworld.org/oregonwolfe ; http://wheat.pw.usda.gov/ggpages/OWB_gallery/ISS-OWB/index.htm). The population of 94 doubled haploid lines was developed from an F1 of a cross between dominant and reces...

Dynamic Conservation of Date Palms: The Future of a Genetic Resource at the Nexus of Climate Change, Desertification and Salinity Stress in Oasis Ecosystems

USDA-ARS?s Scientific Manuscript database

The date palm (Phoenix dactylifera) is the only indigenous, wild desert plant definitely domesticated in its native harsh environment, and along with the camel (Camelus dromedarius), was responsible for opening the vast desert territories for human activity and the development of oasis ecosystems, w...

Water and Nutrient Effects on Loblolly Pine Production and Stand Development on a Sandhill Site

Treesearch

H.L. Allen; T. J. Albaugh; Kurt H. Johnsen

2002-01-01

During the last decade, it has become apparent that production rates of pine plantations in the southeastern United States are far below levels that are biologically and economically optimal. By managing genetic and site resource effectively, production rates should exceed 350 ft3/ acre/year on most sites. In effort to better understand the...

Development of fine-leaved Festuca grass populations identified genetic resources having potential for improved forage production and wildfire control in the western United States

USDA-ARS?s Scientific Manuscript database

Drought and heat tolerant fine-leaved fescue (Festuca ssp.) grasses have potential as components in rangeland greenstrips for wildfire control in semi-arid climates. However, such fine-leaved grasses have been difficult to identify because of specific adaptations, lack of late maturity, and often p...

The Hardwood Tree Improvement and Regeneration Center: its strategic plans for sustaining the hardwood resource

Treesearch

Charles H. Michler; Michael J. Bosela; Paula M. Pijut; Keith E. Woeste

2003-01-01

A regional center for hardwood tree improvement, genomics, and regeneration research, development and technology transfer will focus on black walnut, black cherry, northern red oak and, in the future, on other fine hardwoods as the effort is expanded. The Hardwood Tree Improvement and Regeneration Center (HTIRC) will use molecular genetics and genomics along with...

Oil, fatty acid, flavonoid, and resveratrol content variability in FAD2A functional SNP genotypes in the U.S. peanut mini-core collection

USDA-ARS?s Scientific Manuscript database

Peanut seeds contain high amounts of oil and protein as well as some useful bioactive phytochemicals which can contribute to human health. The U.S. peanut mini-core collection is an important genetic resource for improving seed quality and developing new cultivars. Variability of seed chemical compo...

The interface between primary care and pediatric cardiology.

PubMed

Gidding, S S; Rosenthal, A

1984-12-01

Pediatricians and family practitioners share responsibility with pediatric cardiologists for providing these patients with comprehensive medical services. This article serves as a resource for primary care physicians when questions concerning the care of children with heart disease arise. Considered are questions on growth, development, infectious disease, psychosocial issues, pharmacology, contraception and pregnancy, genetic counseling, school, travel, minor surgery, and financial considerations.

Butterfly genomics eclosing.

PubMed

Beldade, P; McMillan, W O; Papanicolaou, A

2008-02-01

Technological and conceptual advances of the last decade have led to an explosion of genomic data and the emergence of new research avenues. Evolutionary and ecological functional genomics, with its focus on the genes that affect ecological success and adaptation in natural populations, benefits immensely from a phylogenetically widespread sampling of biological patterns and processes. Among those organisms outside established model systems, butterflies offer exceptional opportunities for multidisciplinary research on the processes generating and maintaining variation in ecologically relevant traits. Here we highlight research on wing color pattern variation in two groups of Nymphalid butterflies, the African species Bicyclus anynana (subfamily Satyrinae) and species of the South American genus Heliconius (subfamily Heliconiinae), which are emerging as important systems for studying the nature and origins of functional diversity. Growing genomic resources including genomic and cDNA libraries, dense genetic maps, high-density gene arrays, and genetic transformation techniques are extending current gene mapping and expression profiling analysis and enabling the next generation of research questions linking genes, development, form, and fitness. Efforts to develop such resources in Bicyclus and Heliconius underscore the general challenges facing the larger research community and highlight the need for a community-wide effort to extend ongoing functional genomic research on butterflies.

Draft genome of the Peruvian scallop Argopecten purpuratus.

PubMed

Li, Chao; Liu, Xiao; Liu, Bo; Ma, Bin; Liu, Fengqiao; Liu, Guilong; Shi, Qiong; Wang, Chunde

2018-04-01

The Peruvian scallop, Argopecten purpuratus, is mainly cultured in southern Chile and Peru was introduced into China in the last century. Unlike other Argopecten scallops, the Peruvian scallop normally has a long life span of up to 7 to 10 years. Therefore, researchers have been using it to develop hybrid vigor. Here, we performed whole genome sequencing, assembly, and gene annotation of the Peruvian scallop, with an important aim to develop genomic resources for genetic breeding in scallops. A total of 463.19-Gb raw DNA reads were sequenced. A draft genome assembly of 724.78 Mb was generated (accounting for 81.87% of the estimated genome size of 885.29 Mb), with a contig N50 size of 80.11 kb and a scaffold N50 size of 1.02 Mb. Repeat sequences were calculated to reach 33.74% of the whole genome, and 26,256 protein-coding genes and 3,057 noncoding RNAs were predicted from the assembly. We generated a high-quality draft genome assembly of the Peruvian scallop, which will provide a solid resource for further genetic breeding and for the analysis of the evolutionary history of this economically important scallop.

Proceedings of the symposium on isozymes of North American forest trees and forest insects; July 27, 1979; Berkeley, California

Treesearch

M. Thompson Conkle

1981-01-01

These 10 symposium papers discuss gene resource management, basic genetics, genetic variation between and within tree species, genetic variability and growth, comparisons of tree life history characteristics, genetic variation in forest insects, breeding systems, and applied uses of isozymes in breeding programs.

Construction of a high-density high-resolution genetic map and its integration with BAC-based physical map in channel catfish

USDA-ARS?s Scientific Manuscript database

Construction of genetic linkage map is essential for genetic and genomic studies. Recent advances in sequencing and genotyping technologies made it possible to generate high-density and high-resolution genetic linkage maps, especially for the organisms lacking extensive genomic resources. In the pre...

Genetic control of inflorescence architecture in legumes

PubMed Central

Benlloch, Reyes; Berbel, Ana; Ali, Latifeh; Gohari, Gholamreza; Millán, Teresa; Madueño, Francisco

2015-01-01

The architecture of the inflorescence, the shoot system that bears the flowers, is a main component of the huge diversity of forms found in flowering plants. Inflorescence architecture has also a strong impact on the production of fruits and seeds, and on crop management, two highly relevant agronomical traits. Elucidating the genetic networks that control inflorescence development, and how they vary between different species, is essential to understanding the evolution of plant form and to being able to breed key architectural traits in crop species. Inflorescence architecture depends on the identity and activity of the meristems in the inflorescence apex, which determines when flowers are formed, how many are produced and their relative position in the inflorescence axis. Arabidopsis thaliana, where the genetic control of inflorescence development is best known, has a simple inflorescence, where the primary inflorescence meristem directly produces the flowers, which are thus borne in the main inflorescence axis. In contrast, legumes represent a more complex inflorescence type, the compound inflorescence, where flowers are not directly borne in the main inflorescence axis but, instead, they are formed by secondary or higher order inflorescence meristems. Studies in model legumes such as pea (Pisum sativum) or Medicago truncatula have led to a rather good knowledge of the genetic control of the development of the legume compound inflorescence. In addition, the increasing availability of genetic and genomic tools for legumes is allowing to rapidly extending this knowledge to other grain legume crops. This review aims to describe the current knowledge of the genetic network controlling inflorescence development in legumes. It also discusses how the combination of this knowledge with the use of emerging genomic tools and resources may allow rapid advances in the breeding of grain legume crops. PMID:26257753

An ultra-high-density map as a community resource for discerning the genetic basis of quantitative traits in maize

USDA-ARS?s Scientific Manuscript database

In this study, we generated a linkage map containing 1,151,856 high quality SNPs between Mo17 and B73, which were verified in the maize intermated B73'×'Mo17 (IBM) Syn10 population. This resource is an excellent complement to existing maize genetic maps available in an online database (iPlant, http:...

The Forest Genetic Resources Working Group of the North American Forestry Commission (FAO)

Treesearch

Ronald C. Schmidtling

2002-01-01

The Forest Genetic Resources Working Group (FGRWG) is one of seven working groups established by the North American Forest Commission (NAFC). The NAFC is one of six Forest Commissions established by the Food and Agriculture Organization (F-40). The FGRWG was established by the NAFC in 1961 as the Working Group on Forest Tree Improvement but went through several-changes...

Improving amphibian genomic resources: a multitissue reference transcriptome of an iconic invader.

PubMed

Richardson, Mark F; Sequeira, Fernando; Selechnik, Daniel; Carneiro, Miguel; Vallinoto, Marcelo; Reid, Jack G; West, Andrea J; Crossland, Michael R; Shine, Richard; Rollins, Lee A

2018-01-01

Cane toads (Rhinella marina) are an iconic invasive species introduced to 4 continents and well utilized for studies of rapid evolution in introduced environments. Despite the long introduction history of this species, its profound ecological impacts, and its utility for demonstrating evolutionary principles, genetic information is sparse. Here we produce a de novo transcriptome spanning multiple tissues and life stages to enable investigation of the genetic basis of previously identified rapid phenotypic change over the introduced range. Using approximately 1.9 billion reads from developing tadpoles and 6 adult tissue-specific cDNA libraries, as well as a transcriptome assembly pipeline encompassing 100 separate de novo assemblies, we constructed 62 202 transcripts, of which we functionally annotated ∼50%. Our transcriptome assembly exhibits 90% full-length completeness of the Benchmarking Universal Single-Copy Orthologs data set. Robust assembly metrics and comparisons with several available anuran transcriptomes and genomes indicate that our cane toad assembly is one of the most complete anuran genomic resources available. This comprehensive anuran transcriptome will provide a valuable resource for investigation of genes under selection during invasion in cane toads, but will also greatly expand our general knowledge of anuran genomes, which are underrepresented in the literature. The data set is publically available in NCBI and GigaDB to serve as a resource for other researchers. © The Authors 2017. Published by Oxford University Press.

Improving amphibian genomic resources: a multitissue reference transcriptome of an iconic invader

PubMed Central

Reid, Jack G; Crossland, Michael R

2018-01-01

Abstract Background Cane toads (Rhinella marina) are an iconic invasive species introduced to 4 continents and well utilized for studies of rapid evolution in introduced environments. Despite the long introduction history of this species, its profound ecological impacts, and its utility for demonstrating evolutionary principles, genetic information is sparse. Here we produce a de novo transcriptome spanning multiple tissues and life stages to enable investigation of the genetic basis of previously identified rapid phenotypic change over the introduced range. Findings Using approximately 1.9 billion reads from developing tadpoles and 6 adult tissue-specific cDNA libraries, as well as a transcriptome assembly pipeline encompassing 100 separate de novo assemblies, we constructed 62 202 transcripts, of which we functionally annotated ∼50%. Our transcriptome assembly exhibits 90% full-length completeness of the Benchmarking Universal Single-Copy Orthologs data set. Robust assembly metrics and comparisons with several available anuran transcriptomes and genomes indicate that our cane toad assembly is one of the most complete anuran genomic resources available. Conclusions This comprehensive anuran transcriptome will provide a valuable resource for investigation of genes under selection during invasion in cane toads, but will also greatly expand our general knowledge of anuran genomes, which are underrepresented in the literature. The data set is publically available in NCBI and GigaDB to serve as a resource for other researchers. PMID:29186423

Mouse Models for Drug Discovery. Can New Tools and Technology Improve Translational Power?

PubMed

Zuberi, Aamir; Lutz, Cathleen

2016-12-01

The use of mouse models in biomedical research and preclinical drug evaluation is on the rise. The advent of new molecular genome-altering technologies such as CRISPR/Cas9 allows for genetic mutations to be introduced into the germ line of a mouse faster and less expensively than previous methods. In addition, the rapid progress in the development and use of somatic transgenesis using viral vectors, as well as manipulations of gene expression with siRNAs and antisense oligonucleotides, allow for even greater exploration into genomics and systems biology. These technological advances come at a time when cost reductions in genome sequencing have led to the identification of pathogenic mutations in patient populations, providing unprecedented opportunities in the use of mice to model human disease. The ease of genetic engineering in mice also offers a potential paradigm shift in resource sharing and the speed by which models are made available in the public domain. Predictively, the knowledge alone that a model can be quickly remade will provide relief to resources encumbered by licensing and Material Transfer Agreements. For decades, mouse strains have provided an exquisite experimental tool to study the pathophysiology of the disease and assess therapeutic options in a genetically defined system. However, a major limitation of the mouse has been the limited genetic diversity associated with common laboratory mice. This has been overcome with the recent development of the Collaborative Cross and Diversity Outbred mice. These strains provide new tools capable of replicating genetic diversity to that approaching the diversity found in human populations. The Collaborative Cross and Diversity Outbred strains thus provide a means to observe and characterize toxicity or efficacy of new therapeutic drugs for a given population. The combination of traditional and contemporary mouse genome editing tools, along with the addition of genetic diversity in new modeling systems, are synergistic and serve to make the mouse a better model for biomedical research, enhancing the potential for preclinical drug discovery and personalized medicine. © The Author 2016. Published by Oxford University Press.

Fort Collins Science Center: Species and Habitats of Federal Interest

USGS Publications Warehouse

Stevens, Patty

2004-01-01

Ecosystem changes directly affect a wide variety of plant and animal species, floral and faunal communities, and groups of species such as amphibians and grassland birds. Appropriate management of public lands plays a crucial role in the conservation and recovery of endangered species and can be a key element in preventing a species from being listed under the Endangered Species Act. The Species and Habitats of Federal Interest Branch of the Fort Collins Science Center (FORT) conducts research on the ecology, habitat requirements, distribution and abundance, population dynamics, and genetics and systematics of many species facing threatened or endangered status or of special concern to resource management agencies. FORT scientists develop reintroduction and restoration techniques, technologies for monitoring populations, and novel methods to analyze data on population trends and habitat requirements. FORT expertise encompasses both traditional and specialized natural resource disciplines within wildlife biology, including population dynamics, animal behavior, plant and community ecology, inventory and monitoring, statistics and computer applications, conservation genetics, stable isotope analysis, and curatorial expertise.

A Review on Current Status and Future Prospects of Winged Bean (Psophocarpus tetragonolobus) in Tropical Agriculture.

PubMed

Lepcha, Patrush; Egan, Ashley N; Doyle, Jeff J; Sathyanarayana, N

2017-09-01

Winged bean, Psophocarpus tetragonolobus (L.) DC., is analogous to soybean in yield and nutritional quality, proving a valuable alternative to soybean in tropical regions of the world. The presence of anti-nutritional factors and high costs associated with indeterminate plant habit have been major concerns in this crop. But occurrence of good genetic variability in germplasm collections offers precious resources for winged bean breeding. However, lack of germplasm characterization is hindering such efforts. From a genomic standpoint, winged bean has been little studied despite rapid advancement in legume genomics in the last decade. Exploiting modern genomics/breeding approaches for genetic resource characterization and the breeding of early maturing, high yielding, determinate varieties which are disease resistant and free of anti-nutritional factors along with developing consumer friendly value-added products of local significance are great challenges and opportunities in the future that would boost cultivation of winged bean in the tropics. We review past efforts and future prospects towards winged bean improvement.

A Mesoamerican origin of cherimoya (Annona cherimola Mill.): Implications for the conservation of plant genetic resources.

PubMed

Larranaga, N; Albertazzi, F J; Fontecha, G; Palmieri, M; Rainer, H; van Zonneveld, M; Hormaza, J I

2017-08-01

Knowledge on the structure and distribution of genetic diversity is a key aspect to plan and execute an efficient conservation and utilization of the genetic resources of any crop as well as for determining historical demographic inferences. In this work, a large data set of 1,765 accessions of cherimoya (Annona cherimola Mill, Annonaceae), an underutilized fruit tree crop native to the Neotropics and used as a food source by pre-Columbian cultures, was collected from six different countries across the American continent and amplified with nine highly informative microsatellite markers. The structure analyses, fine representation of the genetic diversity and an ABC approach suggest a Mesoamerican origin of the crop, contrary to previous reports, with clear implications for the dispersion of plant germplasm between Central and South America in pre-Columbian times. These results together with the potential distribution of the species in a climatic change context using two different climate models provide new insights for the history and conservation of extant genetic resources of cherimoya that can be applied to other currently underutilized woody perennial crops. © 2017 John Wiley & Sons Ltd.

Genome resource banking for wildlife research, management, and conservation.

PubMed

Wildt, D E

2000-01-01

Cryobiology offers an important opportunity to assist in the management and study of wildlife, including endangered species. The benefits of developing genome resource banks for wildlife are profound, perhaps more so than for traditional uses in terms of livestock and human fertility. In addition to preserving heterozygosity and assisting in the genetic management of rare populations held in captivity, frozen repositories help insure wild populations against natural and human-induced catastrophes. Such banks also are an invaluable source of new knowledge (for basic and applied research) from thousands of species that have yet to be studied. However, it is crucial that genome resource banks for wildlife species be developed in a coordinated fashion that first benefits the conservation of biodiversity. Spurious collections will be of no advantage to genuine conservation. The Conservation Breeding Specialist Group (CBSG; of the International Union for the Conservation of Nature and Natural Resources' Species Survival Commission) has promoted international dialogue on this topic. CBSG working groups have recognized that such repositories be developed according to specific, scientific guidelines consistent with an international standard that ensures practicality, high-quality ethics, and cost-effectiveness. Areas requiring priority attention also are reviewed, including the need for more basic research, advocacy, and support for developing organized repositories of biomaterials representing the world's diverse biota.

Genetic structure and diversity of indigenous rice (Oryza sativa) varieties in the Eastern Himalayan region of Northeast India.

PubMed

Choudhury, Baharul; Khan, Mohamed Latif; Dayanandan, Selvadurai

2013-12-01

The Eastern Himalayan region of Northeast (NE) India is home to a large number of indigenous rice varieties, which may serve as a valuable genetic resource for future crop improvement to meet the ever-increasing demand for food production. However, these varieties are rapidly being lost due to changes in land-use and agricultural practices, which favor agronomically improved varieties. A detailed understanding of the genetic structure and diversity of indigenous rice varieties is crucial for efficient utilization of rice genetic resources and for developing suitable conservation strategies. To explore the genetic structure and diversity of rice varieties in NE India, we genotyped 300 individuals of 24 indigenous rice varieties representing sali, boro, jum and glutinous types, 5 agronomically improved varieties, and one wild rice species (O. rufipogon) using seven SSR markers. A total of 85 alleles and a very high level of gene diversity (0.776) were detected among the indigenous rice varieties of the region. Considerable level of genetic variation was found within indigenous varieties whereas improved varieties were monoporphic across all loci. The comparison of genetic diversity among different types of rice revealed that sali type possessed the highest gene diversity (0.747) followed by jum (0.627), glutinous (0.602) and boro (0.596) types of indigenous rice varieties, while the lowest diversity was detected in agronomically improved varieties (0.459). The AMOVA results showed that 66% of the variation was distributed among varieties indicating a very high level of genetic differentiation in rice varieties in the region. Two major genetically defined clusters corresponding to indica and japonica groups were detected in rice varieties of the region. Overall, traditionally cultivated indigenous rice varieties in NE India showed high levels of genetic diversity comparable to levels of genetic diversity reported from wild rice populations in various parts of the world. The efforts for conservation of rice germplasm in NE India should consider saving rice varieties representing different types with specific emphasis given to sali and jum types. The protection against the loss of vast genetic diversity found in indigenous rice varieties in NE India is crucial for maintaining future food security in the changing world.

Creating single-copy genetic circuits

PubMed Central

Lee, Jeong Wook; Gyorgy, Andras; Cameron, D. Ewen; Pyenson, Nora; Choi, Kyeong Rok; Way, Jeffrey C.; Silver, Pamela A.; Del Vecchio, Domitilla; Collins, James J.

2017-01-01

SUMMARY Synthetic biology is increasingly used to develop sophisticated living devices for basic and applied research. Many of these genetic devices are engineered using multi-copy plasmids, but as the field progresses from proof-of-principle demonstrations to practical applications, it is important to develop single-copy synthetic modules that minimize consumption of cellular resources and can be stably maintained as genomic integrants. Here we use empirical design, mathematical modeling and iterative construction and testing to build single-copy, bistable toggle switches with improved performance and reduced metabolic load that can be stably integrated into the host genome. Deterministic and stochastic models led us to focus on basal transcription to optimize circuit performance and helped to explain the resulting circuit robustness across a large range of component expression levels. The design parameters developed here provide important guidance for future efforts to convert functional multi-copy gene circuits into optimized single-copy circuits for practical, real-world use. PMID:27425413

Chloroplast genome resources and molecular markers differentiate rubber dandelion species from weedy relatives.

PubMed

Zhang, Yingxiao; Iaffaldano, Brian J; Zhuang, Xiaofeng; Cardina, John; Cornish, Katrina

2017-02-02

Rubber dandelion (Taraxacum kok-saghyz, TK) is being developed as a domestic source of natural rubber to meet increasing global demand. However, the domestication of TK is complicated by its colocation with two weedy dandelion species, Taraxacum brevicorniculatum (TB) and the common dandelion (Taraxacum officinale, TO). TB is often present as a seed contaminant within TK accessions, while TO is a pandemic weed, which may have the potential to hybridize with TK. To discriminate these species at the molecular level, and facilitate gene flow studies between the potential rubber crop, TK, and its weedy relatives, we generated genomic and marker resources for these three dandelion species. Complete chloroplast genome sequences of TK (151,338 bp), TO (151,299 bp), and TB (151,282 bp) were obtained using the Illumina GAII and MiSeq platforms. Chloroplast sequences were analyzed and annotated for all the three species. Phylogenetic analysis within Asteraceae showed that TK has a closer genetic distance to TB than to TO and Taraxacum species were most closely related to lettuce (Lactuca sativa). By sequencing multiple genotypes for each species and testing variants using gel-based methods, four chloroplast Single Nucleotide Polymorphism (SNP) variants were found to be fixed between TK and TO in large populations, and between TB and TO. Additionally, Expressed Sequence Tag (EST) resources developed for TO and TK permitted the identification of five nuclear species-specific SNP markers. The availability of chloroplast genomes of these three dandelion species, as well as chloroplast and nuclear molecular markers, will provide a powerful genetic resource for germplasm differentiation and purification, and the study of potential gene flow among Taraxacum species.

Genetic diversity in Gossypium genus

USDA-ARS?s Scientific Manuscript database

The overall objectives of this paper are to report on cotton germplasm resources, morphobiological and agronomic diversity of Gossypium genus and review efforts on molecular genetic diversity of cotton gene pools as well as on the challenges and perspectives of exploiting genetic diversity in cotton...

Methods of analysis and resources available for genetic trait mapping.

PubMed

Ott, J

1999-01-01

Methods of genetic linkage analysis are reviewed and put in context with other mapping techniques. Sources of information are outlined (books, web sites, computer programs). Special consideration is given to statistical problems in canine genetic mapping (heterozygosity, inbreeding, marker maps).

Genetic structure of Tribolium castaneum (Coleptera: Tenebrionidae) populations in mills

USDA-ARS?s Scientific Manuscript database

The red flour beetle, Tribolium castaneum, is primarily found associated with human structures such as wheat and rice mills, which are spatially isolated resource patches with apparently limited immigration that could produce genetically structured populations. We investigated genetic diversity and...