scholarly journals Genetic factors underlying boron toxicity tolerance in rice: genome-wide association study and transcriptomic analysis

2016 ◽  
pp. erw423 ◽  
Author(s):  
Joao Braga de Abreu Neto ◽  
María Clara Hurtado-Perez ◽  
Monika A. Wimmer ◽  
Michael Frei
Keyword(s):  
Association Study ◽  
Genetic Factors ◽  
Genome Wide Association Study ◽  
Rice Genome ◽  
Transcriptomic Analysis ◽  
Genome Wide Association ◽  
Boron Toxicity ◽  
Genome Wide

scholarly journals A Genome-Wide Association Study Reveals Candidate Genes Related to Salt Tolerance in Rice (Oryza sativa) at the Germination Stage

2018 ◽  
Vol 19 (10) ◽  
pp. 3145 ◽  
Author(s):  
Jie Yu ◽  
Weiguo Zhao ◽  
Wei Tong ◽  
Qiang He ◽  
Min-Young Yoon ◽  
...  
Keyword(s):  
Salt Tolerance ◽  
Association Study ◽  
Candidate Genes ◽  
Genome Wide Association Study ◽  
Rice Genome ◽  
Genome Wide Association ◽  
Phenotypic Correlation ◽  
Genome Wide ◽  
A Genome ◽  
Germination Stage

Salt toxicity is the major factor limiting crop productivity in saline soils. In this paper, 295 accessions including a heuristic core set (137 accessions) and 158 bred varieties were re-sequenced and ~1.65 million SNPs/indels were used to perform a genome-wide association study (GWAS) of salt-tolerance-related phenotypes in rice during the germination stage. A total of 12 associated peaks distributed on seven chromosomes using a compressed mixed linear model were detected. Determined by linkage disequilibrium (LD) blocks analysis, we finally obtained a total of 79 candidate genes. By detecting the highly associated variations located inside the genic region that overlapped with the results of LD block analysis, we characterized 17 genes that may contribute to salt tolerance during the seed germination stage. At the same time, we conducted a haplotype analysis of the genes with functional variations together with phenotypic correlation and orthologous sequence analyses. Among these genes, OsMADS31, which is a MADS-box family transcription factor, had a down-regulated expression under the salt condition and it was predicted to be involved in the salt tolerance at the rice germination stage. Our study revealed some novel candidate genes and their substantial natural variations in the rice genome at the germination stage. The GWAS in rice at the germination stage would provide important resources for molecular breeding and functional analysis of the salt tolerance during rice germination.

scholarly journals Identification of genetic factors controlling phosphorus utilization efficiency in wheat by genome-wide association study with principal component analysis

2020 ◽  
Author(s):  
Luqman Bin Safdar ◽  
Muhammad Jawad Umer ◽  
Fakhrah Almas ◽  
Siraj Uddin ◽  
Qurra-tul-Ain Safdar ◽  
...  
Keyword(s):  
Association Study ◽  
Candidate Genes ◽  
Genetic Factors ◽  
Genome Wide Association Study ◽  
Principal Component ◽  
Utilization Efficiency ◽  
Genome Wide Association ◽  
Genome Wide ◽  
P Utilization ◽  
P Utilization Efficiency

ABSTRACTDespite the economic importance of P utilization efficiency, information on genetic factors underlying this trait remains elusive. To address that, we performed a genome-wide association study in a spring wheat diversity panel ranging from landraces to elite varieties. We evaluated the phenotype variation for P utilization efficiency in controlled conditions and genotype variation using wheat 90K SNP array. Phenotype variables were transformed into a smaller set of uncorrelated principal components that captured the most important variation data. We identified two significant loci associated with both P utilization efficiency and the 1st principal component on chromosomes 3A and 4A: qPE1-3A and qPE2-4A. Annotation of genes at these loci revealed 53 wheat genes, among which 6 were identified in significantly enriched pathways. The expression pattern of these 6 genes indicated that TraesCS4A02G481800, involved in pyruvate metabolism and TCA cycle, had a significantly higher expression in the P efficient variety under limited P conditions. Further characterization of these loci and candidate genes can help stimulate P utilization efficiency in wheat.KEY MESSAGEWe report two new loci for P utilization efficiency on chromosomes 3A and 4A of wheat. The prioritized candidate genes at these loci can be investigated by molecular biology techniques to improve P efficiency in wheat and grass relatives.

scholarly journals 0004 GENOME-WIDE ASSOCIATION STUDY FOR SNORING IDENTIFIES NOVEL GENETIC FACTORS AND BIOLOGICAL LINKS TO SLEEP APNEA AND OBESITY

SLEEP ◽  
2017 ◽  
Vol 40 (suppl_1) ◽  
pp. A2-A2 ◽  
Author(s):  
JM Lane ◽  
I Vlasac ◽  
S Redline ◽  
D Ray ◽  
M Rutter ◽  
...  
Keyword(s):  
Sleep Apnea ◽  
Association Study ◽  
Genetic Factors ◽  
Genome Wide Association Study ◽  
Genome Wide Association ◽  
Genome Wide

scholarly journals Genome-Wide Association Study Reveals the QTLs for Seed Storability in World Rice Core Collections

Plants ◽  
2021 ◽  
Vol 10 (4) ◽  
pp. 812
Author(s):  
Fangxi Wu ◽  
Xi Luo ◽  
Lingqiang Wang ◽  
Yidong Wei ◽  
Jianguo Li ◽  
...  
Keyword(s):  
Association Study ◽  
Genome Wide Association Study ◽  
Rice Genome ◽  
Genome Wide Association ◽  
Rice Seed ◽  
Core Collections ◽  
Genome Wide ◽  
A Genome ◽  
New Varieties ◽  
Seed Storability

Seed storability is a main agronomically important trait to assure storage safety of grain and seeds in rice. Although many quantitative trait loci (QTLs) and associated genes for rice seed storability have been identified, the detailed genetic mechanisms of seed storability remain unclear in rice. In this study, a genome-wide association study (GWAS) was performed in 456 diverse rice core collections from the 3K rice genome. We discovered the new nine QTLs designated as qSS1-1, qSS1-2, qSS2-1, qSS3-1, qSS5-1, qSS5-2, qSS7-1, qSS8-1, and qSS11-1. According to the analysis of the new nine QTLs, our results could well explain the reason why seed storability of indica subspecies was superior to japonica subspecies in rice. Among them, qSS1-2 and qSS8-1 were potentially co-localized with a known associated qSS1/OsGH3-2 and OsPIMT1, respectively. Our results also suggest that pyramiding breeding of superior alleles of these associated genes will lead to new varieties with improved seed storability in the future.

scholarly journals A genome-wide association study of quantitative computed tomographic emphysema in Korean populations

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Sooim Sin ◽  
Hye-Mi Choi ◽  
Jiwon Lim ◽  
Jeeyoung Kim ◽  
So Hyeon Bak ◽  
...  
Keyword(s):  
Gene Expression ◽  
Association Study ◽  
Genetic Factors ◽  
Genome Wide Association Study ◽  
Genome Wide Association ◽  
Candidate Snps ◽  
Copd Patients ◽  
Genome Wide ◽  
A Genome ◽  
Novel Snp

AbstractEmphysema is an important feature of chronic obstructive pulmonary disease (COPD). Genetic factors likely affect emphysema pathogenesis, but this question has predominantly been studied in those of European ancestry. In this study, we sought to determine genetic components of emphysema severity and characterize the potential function of the associated loci in Korean population. We performed a genome-wide association study (GWAS) on quantitative emphysema in subjects with or without COPD from two Korean COPD cohorts. We investigated the functional consequences of the loci using epigenetic annotation and gene expression data. We also compared our GWAS results with an epigenome-wide association study and previous differential gene expression analysis. In total, 548 subjects (476 [86.9%] male) including 514 COPD patients were evaluated. We identified one genome-wide significant SNP (P < 5.0 × 10–8), rs117084279, near PIBF1. We identified an additional 57 SNPs (P < 5.0 × 10–6) associated with emphysema in all subjects, and 106 SNPs (P < 5.0 × 10–6) in COPD patients. Of these candidate SNPs, 2 (rs12459249, rs11667314) near CYP2A6 were expression quantitative trait loci in lung tissue and a SNP (rs11214944) near NNMT was an expression quantitative trait locus in whole blood. Of note, rs11214944 was in linkage disequilibrium with variants in enhancer histone marks in lung tissue. Several genes near additional SNPs were identified in our previous EWAS study with nominal level of significance. We identified a novel SNP associated with quantitative emphysema on CT. Including the novel SNP, several candidate SNPs in our study may provide clues to the genetic etiology of emphysema in Asian populations. Further research and validation of the loci will help determine the genetic factors for the development of emphysema.

scholarly journals Genome-wide association study of genetic factors related to confectionery intake: Potential roles of theADIPOQgene

Obesity ◽  
2013 ◽  
Vol 21 (11) ◽  
pp. 2413-2419 ◽  
Author(s):  
Kenji Wakai ◽  
Keitaro Matsuo ◽  
Fumihiko Matsuda ◽  
Ryo Yamada ◽  
Meiko Takahashi ◽  
...  
Keyword(s):  
Association Study ◽  
Genetic Factors ◽  
Genome Wide Association Study ◽  
Genome Wide Association ◽  
Genome Wide

scholarly journals Genome-wide association study identifies genetic factors that modify age at onset in Machado-Joseph disease

2019 ◽  
Author(s):  
Fulya Akçimen ◽  
Sandra Martins ◽  
Calwing Liao ◽  
Cynthia V. Bourassa ◽  
Hélène Catoire ◽  
...  
Keyword(s):  
Association Study ◽  
Genetic Factors ◽  
Genome Wide Association Study ◽  
Age At Onset ◽  
Cag Repeat ◽  
Genome Wide Association ◽  
Modifying Factors ◽  
Genome Wide ◽  
A Genome ◽  
Machado Joseph Disease

AbstractMachado-Joseph disease (MJD/SCA3) is the most common form of dominantly inherited ataxia worldwide. The disorder is caused by an expanded CAG repeat in the ATXN3 gene. Past studies have revealed that the length of the expansion partly explains the disease age at onset (AO) variability of MJD, which is confirmed in this study. Using a total of 786 MJD patients from five different geographical origins, a genome-wide association study (GWAS) was conducted to identify additional AO modifying factors that could explain some of the residual AO variability. We identified nine suggestively associated loci (P < 1 × 10−5). These loci were enriched for genes involved in vesicle transport, olfactory signaling, and synaptic pathways. Furthermore, associations between AO and the TRIM29 and RAG genes suggests that DNA repair mechanisms might be implicated in MJD pathogenesis. Our study demonstrates the existence of several additional genetic factors, along with CAG expansion, that may lead to a better understanding of the genotype-phenotype correlation in MJD.

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