scholarly journals Genome-Wide Association Study of Actinidia Chinensis

2020 ◽  
Author(s):  
Yu Zhang ◽  
Yuexing Wang ◽  
Shimao Zheng ◽  
Wanying Zhou ◽  
Wenhui Zhang ◽  
...  
Keyword(s):  
Metabolic Pathways ◽  
Haplotype Analysis ◽  
Genome Wide Association Study ◽  
Genome Wide Association ◽  
Actinidia Chinensis ◽  
Analysis Of Molecular Variance ◽  
Growth Environment ◽  
Molecular Variance ◽  
Genome Wide ◽  
Two Populations

Abstract Background: A total of 74,936 SNPs were employed to carry out GWAS and post-GWAS of the fifty-six accessions, representing the two most valuable varieties of Actinidia chinensis, namely, A. chinensis var. chinensis and A. chinensis var. deliciosa, are mainly distributed in China. The percentage of heterozygous sites of A. chinensis var. deliciosa is higher than that of A. chinensis var. chinensis, which could be one of the reasons for A. chinensis var. deliciosa high disease resistance. LD decay distance of male plants is shorter than that of female plants. Results: Fifty-six accessions were divided into two subgroups. Analysis of molecular variance shows that the frequency of genetic variations within the population is 83.53% and 16.47% between populations. Fst between the two populations is 0.14, and Nm is 1.60. Set at α ≤ 0.05, a total of 327 SNPs and 260 haplotypes were related to the hispidus. A total of 246 proteins were annotated using GO and KEGG analyses, which indicated the membrane-related genes and stress-resistant metabolic pathways are related to the hispidus condition of leaves, stems, and peels of kiwifruit, which is also the result of the adaptation of A. chinensis var. deliciosa to its growth environment. Conclusions: Haplotype analysis showed that the evolution of is A. chinensis var. deliciosa later than that of A. chinensis var. chinensis.

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 A Genome-Wide Association Study for Agronomic Traits in Soybean Using SNP Markers and SNP-Based Haplotype Analysis

PLoS ONE ◽  
2017 ◽  
Vol 12 (2) ◽  
pp. e0171105 ◽  
Author(s):  
Rodrigo Iván Contreras-Soto ◽  
Freddy Mora ◽  
Marco Antônio Rott de Oliveira ◽  
Wilson Higashi ◽  
Carlos Alberto Scapim ◽  
...  
Keyword(s):  
Association Study ◽  
Haplotype Analysis ◽  
Genome Wide Association Study ◽  
Agronomic Traits ◽  
Snp Markers ◽  
Genome Wide Association ◽  
Genome Wide ◽  
A Genome

scholarly journals Genome-wide association study reveals the genetic architecture of root hair length in maize

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Lin Liu ◽  
Lu-Guang Jiang ◽  
Jin-Hong Luo ◽  
Ai-Ai Xia ◽  
Li-Qun Chen ◽  
...  
Keyword(s):  
Root Hair ◽  
Metabolic Pathways ◽  
Hair Growth ◽  
Genetic Basis ◽  
Genome Wide Association Study ◽  
Genome Wide Association ◽  
Hair Length ◽  
Root Hair Length ◽  
Genome Wide ◽  
Root Hair Growth

Abstract Background Root hair, a special type of tubular-shaped cell, outgrows from root epidermal cell and plays important roles in the acquisition of nutrients and water, as well as interactions with biotic and abiotic stress. Although many genes involved in root hair development have been identified, genetic basis of natural variation in root hair growth has never been explored. Results Here, we utilized a maize association panel including 281 inbred lines with tropical, subtropical, and temperate origins to decipher the phenotypic diversity and genetic basis of root hair length. We demonstrated significant associations of root hair length with many metabolic pathways and other agronomic traits. Combining root hair phenotypes with 1.25 million single nucleotide polymorphisms (SNPs) via genome-wide association study (GWAS) revealed several candidate genes implicated in cellular signaling, polar growth, disease resistance and various metabolic pathways. Conclusions These results illustrate the genetic basis of root hair length in maize, offering a list of candidate genes predictably contributing to root hair growth, which are invaluable resource for the future functional investigation.

scholarly journals Genome-Wide Association Study for Squalene Contents and Functional Haplotype Analysis in Rice

ACS Omega ◽  
2019 ◽  
Vol 4 (21) ◽  
pp. 19358-19365
Author(s):  
Xiao-Qiang Wang ◽  
Kyu-Won Kim ◽  
Sang-Ho Chu ◽  
Rungnapa Phitaktansakul ◽  
Sang-Won Park ◽  
...  
Keyword(s):  
Association Study ◽  
Haplotype Analysis ◽  
Genome Wide Association Study ◽  
Genome Wide Association ◽  
Genome Wide

Genome wide association study on memory in schizophrenia patients and unaffected probands

2009 ◽  
Vol 42 (05) ◽  
Author(s):  
B Konte ◽  
I Giegling ◽  
AM Hartmann ◽  
H Konnerth ◽  
P Muglia ◽  
...  
Keyword(s):  
Association Study ◽  
Genome Wide Association Study ◽  
Genome Wide Association ◽  
Genome Wide
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