Haplotype Analysis of Complex Traits in Outcrossing Tree Species

2011 ◽  
pp. 62-84
Author(s):  
Tian Liu ◽  
Chunfa Tong ◽  
Jiangtao Luo ◽  
Jiasheng Wu ◽  
Bo Zhang ◽  
...  
Keyword(s):  
Tree Species ◽  
Complex Traits ◽  
Haplotype Analysis

scholarly journals Genome-wide haplotype association study in imaging genetics using whole-brain sulcal openings of 16,304 UK Biobank subjects

2021 ◽  
Author(s):  
Slim Karkar ◽  
Claire Dandine-Roulland ◽  
Jean-François Mangin ◽  
Yann Le Guen ◽  
Cathy Philippe ◽  
...  
Keyword(s):  
Brain Imaging ◽  
Complex Traits ◽  
Haplotype Analysis ◽  
Imaging Genetics ◽  
Genetic Maps ◽  
Imaging Features ◽  
Uk Biobank ◽  
Whole Brain ◽  
Genome Wide ◽  
A Genome

AbstractNeuroimaging-genetics cohorts gather two types of data: brain imaging and genetic data. They allow the discovery of associations between genetic variants and brain imaging features. They are invaluable resources to study the influence of genetics and environment in the brain features variance observed in normal and pathological populations. This study presents a genome-wide haplotype analysis for 123 brain sulcus opening value (a measure of sulcal width) across the whole brain that include 16,304 subjects from UK Biobank. Using genetic maps, we defined 119,548 blocks of low recombination rate distributed along the 22 autosomal chromosomes and analyzed 1,051,316 haplotypes. To test associations between haplotypes and complex traits, we designed three statistical approaches. Two of them use a model that includes all the haplotypes for a single block, while the last approach considers each haplotype independently. All the statistics produced were assessed as rigorously as possible. Thanks to the rich imaging dataset at hand, we used resampling techniques to assess False Positive Rate for each statistical approach in a genome-wide and brain-wide context. The results on real data show that genome-wide haplotype analyses are more sensitive than single-SNP approach and account for local complex Linkage Disequilibrium (LD) structure, which makes genome-wide haplotype analysis an interesting and statistically sound alternative to the single-SNP counterpart.

scholarly journals CandiHap: a toolkit for haplotype analysis for sequence of samples and fast identification of candidate causal gene(s) in genome-wide association study

2020 ◽  
Author(s):  
Xukai Li ◽  
Zhiyong Shi ◽  
Qianru Qie ◽  
Jianhua Gao ◽  
Xingchun Wang ◽  
...  
Keyword(s):  
Linkage Disequilibrium ◽  
Association Study ◽  
Complex Traits ◽  
Haplotype Analysis ◽  
Genome Wide Association Study ◽  
Significant Snps ◽  
Causal Variant ◽  
Genome Wide Association ◽  
Causal Gene ◽  
Genome Wide

AbstractGenome-wide association study (GWAS) is widely used to identify genes involved in plants, animals and human complex traits. Generally, the identified SNP is not necessarily the causal variant, but it is rather in linkage disequilibrium (LD). One key challenge for GWAS results interpretation is to rapidly identify causal genes and provide profound evidence on how they affect the trait. Researches want to identify candidate causal variants from the most significant SNPs of GWAS in any species and on their local computer, while to complete these tasks are to be time-consuming, laborious and prone to errors and omission. To our knowledge, so far there is no tool available to solve the challenge for GWAS data very quickly. Based on the standard VCF (variant call format) format, CandiHap is developed to fast preselection candidate causal SNPs and gene(s) from GWAS by integrating LD result, SNP annotation, haplotype analysis and traits statistics of haplotypes. Investigators can specify genes or linkage regions based on GWAS results, linkage disequilibrium (LD), and predicted candidate causal gene(s). It supported Windows, Mac and Linux computers and servers in graphical interface and command line, and applied to any other plant, animal or bacteria species. The source code of CandiHap tool is freely available at https://github.com/xukaili/CandiHap

scholarly journals Genome-wide haplotype association study in imaging genetics using whole-brain sulcal openings of 16,304 UK Biobank subjects

2020 ◽  
Author(s):  
Slim Karkar ◽  
Claire Dandine-Roulland ◽  
Jean-François Mangin ◽  
Yann Le Guen ◽  
Cathy Philippe ◽  
...  
Keyword(s):  
Brain Imaging ◽  
Complex Traits ◽  
Haplotype Analysis ◽  
Imaging Genetics ◽  
Genetic Maps ◽  
Imaging Features ◽  
Uk Biobank ◽  
Whole Brain ◽  
Genome Wide ◽  
A Genome

AbstractNeuroimaging-genetics cohorts gather two types of data: brain imaging and genetic data. They allow the discovery of associations between genetic variants and brain imaging features. They are invaluable resources to study the influence of genetics and environment in the brain features variance observed in normal and pathological populations. This study presents a genome wide haplotype analysis for 123 brain sulcus opening value (a measure of sulcal width) across the whole brain that include 16,304 subjects from UK Biobank. Using genetic maps, we defined 119,548 blocks of low recombination rate distributed along the 22 autosomal chromosomes, and analyzed 1,051,316 haplotypes. To test associations between haplotypes and complex traits, we designed three statistical approaches. Two of them use a model that includes all the haplotypes for a sin gle block, while the last approach considers one model by haplotype. All the statistics produced were assessed as rigorously as possible. Thanks to the rich imaging dataset at hand, we used resampling techniques to assess False Positive Rate for each statistical approach in a genome-wide and brain-wide context. The results on real data show that genome-wide haplotype analyses are more sensitive than single-SNP approach and account for local complex Linkage Disequilibrium (LD) structure, which makes genome-wide haplotype analysis an interesting and statistically sound alternative to the single-SNP counterpart.

scholarly journals Status of perennial tree germplasm resources in India and their utilization in the context of global genome sequencing efforts

2020 ◽  
Author(s):  
Kunasekaran Rajarajan ◽  
◽  
Alka Bharati ◽  
Hirdayesh Anuragi ◽  
Arun Kumar Handa ◽  
...  
Keyword(s):  
Tree Species ◽  
Complex Traits ◽  
Human Life ◽  
Genomic Research ◽  
Diagnostic Tools ◽  
Economic Traits ◽  
Juvenile Period ◽  
High Genetic Diversity ◽  
Widespread Application ◽  
Tree Genomics

Tree species are characterized by their perennial growth habit, woody morphology, long juvenile period phase, mostly outcrossing behaviour, highly heterozygosity genetic makeup, and relatively high genetic diversity. The economically important trees have been an integral part of the human life system due to their provision of timber, fruit, fodder, and medicinal and/or health benefits. Despite its widespread application in agriculture, industrial and medicinal values, the molecular aspects of key economic traits of many tree species remain largely unexplored. Over the past two decades, research on forest tree genomics has generally lagged behind that of other agronomic crops. Genomic research on trees is motivated by the need to support genetic improvement programmes mostly for food trees and timber, and develop diagnostic tools to assist in recommendation for optimum conservation, restoration and management of natural populations. Research on long-lived woody perennials is extending our molecular knowledge and understanding of complex life histories and adaptations to the environment, enriching a field that has traditionally drawn its biological inference from a few short-lived herbaceous species. These concerns have fostered research aimed at deciphering the genomic basis of complex traits that are related to the adaptive value of trees. This review summarizes the highlights of tree genomics and offers some priorities for accelerating progress in the next decade.

Purification of plasma membranes from leaves of conifer and deciduous tree species by phase partitioning and free-flow electrophoresis

1995 ◽  
Vol 95 (3) ◽  
pp. 399-408 ◽  
Author(s):  
Elena Toll ◽  
Federico J. Castillo ◽  
Pierre Crespi ◽  
Michele Crevecoeur ◽  
Hubert Greppin
Keyword(s):  
Tree Species ◽  
Plasma Membranes ◽  
Free Flow ◽  
Deciduous Tree ◽  
Phase Partitioning

Biscogniauxia (Hypoxylon) Canker or Dieback in Trees

EDIS ◽  
2017 ◽  
Vol 2017 (6) ◽  
Author(s):  
Claudia Paez ◽  
Jason A. Smith
Keyword(s):  
Water Stress ◽  
Tree Species ◽  
Soil Compaction ◽  
Urban Areas ◽  
Root Disease ◽  
Poor Health ◽  
Green Spaces ◽  
Opportunistic Pathogens ◽  
Wide Range ◽  
Quercus Spp

Biscogniauxia canker or dieback (formerly called Hypoxylon canker or dieback) is a common contributor to poor health and decay in a wide range of tree species (Balbalian & Henn 2014). This disease is caused by several species of fungi in the genus Biscogniauxia (formerly Hypoxylon). B. atropunctata or B. mediterranea are usually the species found on Quercus spp. and other hosts in Florida, affecting trees growing in many different habitats, such as forests, parks, green spaces and urban areas (McBride & Appel, 2009).  Typically, species of Biscogniauxia are opportunistic pathogens that do not affect healthy and vigorous trees; some species are more virulent than others. However, once they infect trees under stress (water stress, root disease, soil compaction, construction damage etc.) they can quickly colonize the host. Once a tree is infected and fruiting structures of the fungus are evident, the tree is not likely to survive especially if the infection is in the tree's trunk (Anderson et al., 1995).

Climate resilience through natural regeneration in degraded natural forests of south-eastern hilly region of Bangladesh

2019 ◽  
Vol 48 (3) ◽  
pp. 417-425
Author(s):  
Md Khayrul Alam Bhuiyan ◽  
Md Akhter Hossain ◽  
Abdul Kadir Ibne Kamal ◽  
Mohammed Kamal Hossain ◽  
Mohammed Jashimuddin ◽  
...  
Keyword(s):  
Tree Species ◽  
Natural Regeneration ◽  
Diversity Indices ◽  
Acacia Auriculiformis ◽  
Quantitative Structure ◽  
Natural Forests ◽  
Climate Resilience ◽  
Hilly Region ◽  
Major Cluster ◽  
Ecological Dominance

A study was conducted by using 5m × 5m sized 179 quadrates following multistage random sampling method for comparative regenerating tree species, quantitative structure, diversity, similarity and climate resilience in the degraded natural forests and plantations of Cox's Bazar North and South Forest Divisions. A total of 70 regenerating tree species were recorded representing maximum (47 species) from degraded natural forests followed by 43 species from 0.5 year 39 species from 1.5 year and 29 species from 2.5 year old plantations. Quantitative structure relating to ecological dominance indicated dominance of Acacia auriculiformis, Grewia nervosa and Lithocarpus elegans seedlings in the plantations whereas seedlings of Aporosa wallichii, Suregada multiflora and Grewia nervosa in degraded natural forests. The degraded natural forests possess higher natural regeneration potential as showed by different diversity indices. The dominance-based cluster analysis showed 2 major cluster of species under one of which multiple sub-clusters of species exists. Poor plant diversity and presence of regenerating exotic species in the plantations indicated poor climate resilience of forest ecosystem in terms of natural regeneration.

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