Heritability and molecular genetic basis of acoustic startle eye blink and affectively modulated startle response: A genome-wide association study

A genome-wide association study (GWAS) was used to investigate the genetic basis of chilling tolerance in a collection of 117 rice accessions, including 26 Korean landraces and 29 weedy rices, at the reproductive stage. To assess chilling tolerance at the early young microspore stage, plants were treated at 12 °C for 5 days, and tolerance was evaluated using seed set fertility. GWAS, together with principal component analysis and kinship matrix analysis, revealed five quantitative trait loci (QTLs) associated with chilling tolerance on chromosomes 3, 6, and 7. The percentage of phenotypic variation explained by the QTLs was 11–19%. The genomic region underlying the QTL on chromosome 3 overlapped with a previously reported QTL associated with spikelet fertility. Subsequent bioinformatic and haplotype analyses suggested three candidate chilling-tolerance genes within the QTL linkage disequilibrium block: Os03g0305700, encoding a protein similar to peptide chain release factor 2; Os06g0495700, encoding a beta tubulin, autoregulation binding-site-domain-containing protein; and Os07g0137800, encoding a protein kinase, core-domain-containing protein. Further analysis of the detected QTLs and the candidate chilling-tolerance genes will facilitate strategies for developing chilling-tolerant rice cultivars in breeding programs.

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Genome-Wide Association Study of H/L Traits in Chicken

Animals ◽

10.3390/ani9050260 ◽

2019 ◽

Vol 9 (5) ◽

pp. 260 ◽

Cited By ~ 1

Author(s):

Bo Zhu ◽

Qinghe Li ◽

Ranran Liu ◽

Maiqing Zheng ◽

Jie Wen ◽

...

Keyword(s):

Disease Resistance ◽

Association Study ◽

Genetic Basis ◽

Molecular Mechanisms ◽

Genome Wide Association Study ◽

Gene Annotation ◽

Immune Defense ◽

Genome Wide Association ◽

Genome Wide ◽

A Genome

Presently, the heterophil-to-lymphocyte (H/L) ratio is being studied extensively as a disease resistance trait. Through intricate mechanisms to identify and destroy pathogenic microorganisms, heterophils play a pivotal role in the immune defense systems of avian species. To reveal the genetic basis and molecular mechanisms affecting the H/L ratio, phenotypic and H/L data from 1650 white feather chicken broilers were used in performing a genome-wide association study. A self-developed, chicken-specific 55K chip was used for heterophils, lymphocytes, and H/L classification, according to individual genomic DNA profiles. We identified five significant single nucleotide polymorphisms (SNPs) when the genome-wide significance threshold was set to 5% (p < 2.42 × 10−6). A total of 15 SNPs obtained seemingly significant levels (p < 4.84 × 10−5). Gene annotation indicated that CARD11 (Caspase recruitment domain family member 11), BRIX1 (Biogenesis of ribosomes BRX1), and BANP (BTG3 associated nuclear protein) play a role in H/L-associated cell regulation and potentially constitute candidate gene regions for cellular functions dependent on H/L ratios. These results lay the foundation for revealing the genetic basis of disease resistance and future marker-assisted selection for disease resistance.

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A genome-wide association study of susceptibility to acute lymphoblastic leukemia in adolescents and young adults

Blood ◽

10.1182/blood-2014-09-595744 ◽

2015 ◽

Vol 125 (4) ◽

pp. 680-686 ◽

Cited By ~ 65

Author(s):

Virginia Perez-Andreu ◽

Kathryn G. Roberts ◽

Heng Xu ◽

Colton Smith ◽

Hui Zhang ◽

...

Keyword(s):

Acute Lymphoblastic Leukemia ◽

Genetic Basis ◽

Genome Wide Association Study ◽

Lymphoblastic Leukemia ◽

Genome Wide Association ◽

Age Group ◽

Genome Wide ◽

A Genome ◽

Key Points ◽

Similarities And Differences

Key Points In this first ALL GWAS in AYAs, we determined that inherited GATA3 variants strongly influence ALL susceptibility in this age group. These findings revealed similarities and differences in the genetic basis of ALL susceptibility between young children and AYAs.

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Exploring the genetic basis of chronic periodontitis: a genome-wide association study

Human Molecular Genetics ◽

10.1093/hmg/ddt065 ◽

2013 ◽

Vol 22 (11) ◽

pp. 2312-2324 ◽

Cited By ~ 144

Author(s):

K. Divaris ◽

K. L. Monda ◽

K. E. North ◽

A. F. Olshan ◽

L. M. Reynolds ◽

...

Keyword(s):

Association Study ◽

Chronic Periodontitis ◽

Genetic Basis ◽

Genome Wide Association Study ◽

Genome Wide Association ◽

Genome Wide ◽

A Genome

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Genetics of fasting and postprandial metabolite levels are overlapping

Physiological Genomics ◽

10.1152/physiolgenomics.00101.2017 ◽

2018 ◽

Vol 50 (4) ◽

pp. 235-236

Author(s):

Ruifang Li-Gao ◽

Renée de Mutsert ◽

Frits R. Rosendaal ◽

Ko Willems van Dijk ◽

Dennis O. Mook-Kanamori

Keyword(s):

Association Study ◽

Human Body ◽

Genetic Basis ◽

Genome Wide Association Study ◽

Genome Wide Association ◽

Genetic Associations ◽

Mixed Meal ◽

Genome Wide ◽

A Genome ◽

Metabolite Concentrations

In 2015, a genome-wide association study described 59 independent signals that showed strong associations with 85 fasting metabolite concentrations as measured by the Biocrates AbsoluteIDQ p150 kit. However, the human body resides in a nonfasting state for the greater part of the day, and the genetic basis of postprandial metabolite concentrations remains largely unknown. We systematically examined these previously identified genetic associations in postprandial metabolite concentrations after a mixed meal. Of these 85 metabolites, 23 were identified with significant changes after the meal, for which 38 gene-metabolite associations were analyzed. Of these 38 associations, 31 gene-metabolite associations were replicated with postprandial metabolite concentrations. These data indicate that the genetics of fasting and postprandial metabolite levels are significantly overlapping.

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Genome-wide association mapping for high temperature tolerance in wheat through 90k SNP array using physiological and yield traits

PLoS ONE ◽

10.1371/journal.pone.0262569 ◽

2022 ◽

Vol 17 (1) ◽

pp. e0262569

Author(s):

Hafiz Ghulam Muhu-Din Ahmed ◽

Muhammad Naeem ◽

Yawen Zeng ◽

Muhammad Abdul Rehman Rashid ◽

Aziz Ullah ◽

...

Keyword(s):

Heat Stress ◽

Genetic Basis ◽

Genome Wide Association Study ◽

Wheat Yield ◽

Snp Array ◽

Genome Wide Association ◽

Strong Positive Correlation ◽

Yield Traits ◽

Genome Wide ◽

A Genome

Dissecting the genetic basis of physiological and yield traits against tolerance to heat stress is an essential in wheat breeding programs to boost up the wheat yield for sustainable food security. Herein, a genome-wide association study (GWAS) was performed to reveal the genetic basis of heat tolerance using high-density Illumina 90K Infinium SNPs array through physiological and yield indices. These indices were phenotyped on a diverse panel of foreign and domestic genotypes of Pakistan, grown in normal and heat-stressed environments. Based on STRUCTURE analysis, the studied germplasm clustered into four sub-population. Highly significant variations with a range of moderate (58.3%) to high (77.8%) heritability was observed under both conditions. Strong positive correlation existed among physiological and yield related attributes. A total of 320 significant (-log10 P ≥ 3) marker-trait associations (MTAs) were identified for the observed characters. Out of them 169 and 151 MTAs were recorded in normal and heat stress environments, respectively. Among the MTA loci, three (RAC875_c103017_302, Tdurum_contig42087_1199, and Tdurum_contig46877_488 on chromosomes 4B, 6B, and 7B respectively), two (BobWhite_c836_422 and BS00010616_51) and three (Kukri_rep_c87210_361, D_GA8KES401BNLTU_253 and Tdurum_contig1015_131) on chromosomes 5A, 1B, and 3D at the positions 243.59cM, 77.82cM and 292.51cM) showed pleiotropic effects in studied traits under normal, heat-stressed and both conditions respectively. The present study not only authenticated the numerous previously reported MTAs for examined attributes but also revealed novel MTAs under heat-stressed conditions. Identified SNPs will be beneficial in determining the novel genes in wheat to develop the heat tolerant and best yielded genotypes to fulfill the wheat requirement for the growing population.

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