The Genetic Basis of Haploid Induction in Maize Identified with a Novel Genome-Wide Association Method

Increasing the understanding genetic basis of the variability in root system architecture (RSA) is essential to improve resource-use efficiency in agriculture systems and to develop climate-resilient crop cultivars. Roots being underground, their direct observation and detailed characterization are challenging. Here, were characterized twelve RSA-related traits in a panel of 137 early maturing soybean lines (Canadian soybean core collection) using rhizoboxes and two-dimensional imaging. Significant phenotypic variation (P < 0.001) was observed among these lines for different RSA-related traits. This panel was genotyped with 2.18 million genome-wide single-nucleotide polymorphisms (SNPs) using a combination of genotyping-by-sequencing and whole-genome sequencing. A total of 10 quantitative trait locus (QTL) regions were detected for root total length and primary root diameter through a comprehensive genome-wide association study. These QTL regions explained from 15 to 25% of the phenotypic variation and contained two putative candidate genes with homology to genes previously reported to play a role in RSA in other species. These genes can serve to accelerate future efforts aimed to dissect genetic architecture of RSA and breed more resilient varieties.

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Genome-Wide Association Analysis Dissects the Genetic Basis of the Grain Carbon and Nitrogen Contents in Milled Rice

Rice ◽

10.1186/s12284-019-0362-2 ◽

2019 ◽

Vol 12 (1) ◽

Author(s):

Liang Tang ◽

Fan Zhang ◽

Anjin Liu ◽

Jian Sun ◽

Song Mei ◽

...

Keyword(s):

Association Analysis ◽

Genetic Basis ◽

Genome Wide Association ◽

Milled Rice ◽

Genome Wide Association Analysis ◽

Carbon And Nitrogen ◽

Genome Wide ◽

Nitrogen Contents

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Genome-Wide Association Study (GWAS) For Cold Tolerance at The Bud Burst Stage in Rice Using SNP Markers

10.21203/rs.3.rs-311085/v1 ◽

2021 ◽

Author(s):

Caijing Li ◽

Jindong Liu ◽

Jianxin Bian ◽

Tao Jin ◽

Baoli Zou ◽

...

Keyword(s):

Low Temperature ◽

Association Study ◽

Cold Tolerance ◽

Genetic Basis ◽

Genome Wide Association Study ◽

Genome Wide Association ◽

Bud Burst ◽

Rice Varieties ◽

Rice Landraces ◽

Genome Wide

Abstract Background: Rice is a crop that is very sensitive to low temperature, and its morphological development and production are greatly affected by low temperature. Therefore, understanding the genetic basis of cold tolerance in rice is of great significance for mining favorable genes and cultivating excellent rice varieties. However, there were limited studies focusing on cold tolerance at the bud burst stage, therefore, considerable attention should be paid to the genetic basis of cold tolerance at the bud burst stage (CTBB).Results: In this study, a natural population consisting of 211 rice landraces collected from 15 provinces of China and other countries were firstly used to evaluate the cold tolerance at the bud burst stage. Population structure analysis showed that this population divided into three groups and was rich in genetic diversity. Our evaluation results confered that the japonica rice was more tolerance to cold at the bud burst stage than indica rice. Genome-wide association study (GWAS) were performed through the phenotypic data of 211 rice landraces and 36,727 SNPs dataset under a mixed linear model, and 12 QTLs (P < 0.0001) were identified according to the seedling survival rate (SSR) treated at 4 ℃, in which there are five QTLs (qSSR2-2, qSSR3-1, qSSR3-2, qSSR3-3 and qSSR9) which were co-located with previous studies, and seven QTLs (qSSR2-1, qSSR3-4, qSSR3-5, qSSR3-6, qSSR3-7, qSSR4 and qSSR7) which were reported for the first time. Among these QTLs, qSSR9, harboring the highest-peak SNP, explained biggest phenotypic variation. Through bioinformatics analysis, five genes (LOC_Os09g12440, LOC_Os09g12470, LOC_Os09g12520, LOC_Os09g12580 and LOC_Os09g12720) were nominated as candidates for qSSR9. Conclusion: This natural population consisting of 211 rice landraces with high density SNPs will serve as a better choice for identifying rice QTLs/genes in future, and the detected QTLs associated with cold tolerance in rice bud burst stage will be conducive to further mining favorable genes and breeding of rice varieties under cold stress.

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GWAS of three molecular traits highlights core genes and pathways alongside a highly polygenic background

10.1101/2020.04.20.051631 ◽

2020 ◽

Cited By ~ 6

Author(s):

Nasa Sinnott-Armstrong ◽

Sahin Naqvi ◽

Manuel Rivas ◽

Jonathan K Pritchard

Keyword(s):

Complex Traits ◽

Genetic Basis ◽

Association Studies ◽

Genome Wide Association ◽

Genome Wide Association Studies ◽

Biological Processes ◽

Uk Biobank ◽

The Core ◽

Genome Wide ◽

Core Genes

SummaryGenome-wide association studies (GWAS) have been used to study the genetic basis of a wide variety of complex diseases and other traits. However, for most traits it remains difficult to interpret what genes and biological processes are impacted by the top hits. Here, as a contrast, we describe UK Biobank GWAS results for three molecular traits—urate, IGF-1, and testosterone—that are biologically simpler than most diseases, and for which we know a great deal in advance about the core genes and pathways. Unlike most GWAS of complex traits, for all three traits we find that most top hits are readily interpretable. We observe huge enrichment of significant signals near genes involved in the relevant biosynthesis, transport, or signaling pathways. We show how GWAS data illuminate the biology of variation in each trait, including insights into differences in testosterone regulation between females and males. Meanwhile, in other respects the results are reminiscent of GWAS for more-complex traits. In particular, even these molecular traits are highly polygenic, with most of the variance coming not from core genes, but from thousands to tens of thousands of variants spread across most of the genome. Given that diseases are often impacted by many distinct biological processes, including these three, our results help to illustrate why so many variants can affect risk for any given disease.

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Integrating Publicly Available Genome-Wide Association Data to Study the Genetic Basis of Metabolically Healthy Obese and Metabolically Obese but Normal-Weight Individuals

Diabetes ◽

10.2337/db14-1358 ◽

2014 ◽

Vol 63 (12) ◽

pp. 4004-4007 ◽

Cited By ~ 9

Author(s):

R. J. F. Loos

Keyword(s):

Genetic Basis ◽

Normal Weight ◽

Genome Wide Association ◽

Metabolically Healthy Obese ◽

Genome Wide ◽

Healthy Obese ◽

Metabolically Healthy ◽

Association Data

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Common Susceptibility Loci for Male Breast Cancer

JNCI Journal of the National Cancer Institute ◽

10.1093/jnci/djaa101 ◽

2020 ◽

Author(s):

Sarah Maguire ◽

Eleni Perraki ◽

Katarzyna Tomczyk ◽

Michael E Jones ◽

Olivia Fletcher ◽

...

Keyword(s):

Breast Cancer ◽

Association Study ◽

Genetic Correlation ◽

Male Breast Cancer ◽

Genetic Basis ◽

Genome Wide Association Study ◽

Genome Wide Association ◽

Susceptibility Loci ◽

Single Nucleotide ◽

Genome Wide

Abstract Background The etiology of male breast cancer (MBC) is poorly understood. In particular, the extent to which the genetic basis of MBC differs from female breast cancer (FBC) is unknown. A previous genome-wide association study of MBC identified 2 predisposition loci for the disease, both of which were also associated with risk of FBC. Methods We performed genome-wide single nucleotide polymorphism genotyping of European ancestry MBC case subjects and controls in 3 stages. Associations between directly genotyped and imputed single nucleotide polymorphisms with MBC were assessed using fixed-effects meta-analysis of 1380 cases and 3620 controls. Replication genotyping of 810 cases and 1026 controls was used to validate variants with P values less than 1 × 10–06. Genetic correlation with FBC was evaluated using linkage disequilibrium score regression, by comprehensively examining the associations of published FBC risk loci with risk of MBC and by assessing associations between a FBC polygenic risk score and MBC. All statistical tests were 2-sided. Results The genome-wide association study identified 3 novel MBC susceptibility loci that attained genome-wide statistical significance (P < 5 × 10–08). Genetic correlation analysis revealed a strong shared genetic basis with estrogen receptor–positive FBC. Men in the top quintile of genetic risk had a fourfold increased risk of breast cancer relative to those in the bottom quintile (odds ratio = 3.86, 95% confidence interval = 3.07 to 4.87, P = 2.08 × 10–30). Conclusions These findings advance our understanding of the genetic basis of MBC, providing support for an overlapping genetic etiology with FBC and identifying a fourfold high-risk group of susceptible men.

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Genome‐wide association analyses reveal the genetic basis of combining ability in rice

Plant Biotechnology Journal ◽

10.1111/pbi.13134 ◽

2019 ◽

Vol 17 (11) ◽

pp. 2211-2222 ◽

Cited By ~ 4

Author(s):

Junxiao Chen ◽

Hao Zhou ◽

Weibo Xie ◽

Duo Xia ◽

Guanjun Gao ◽

...

Keyword(s):

Combining Ability ◽

Genetic Basis ◽

Genome Wide Association ◽

Association Analyses ◽

Genome Wide

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Genome-wide association study reveals the genetic basis of cold tolerance in wheat

Molecular Breeding ◽

10.1007/s11032-020-01115-x ◽

2020 ◽

Vol 40 (4) ◽

Cited By ~ 2

Author(s):

Yong Zhao ◽

Jiahao Li ◽

Ruiling Zhao ◽

Ke Xu ◽

Yirao Xiao ◽

...

Keyword(s):

Association Study ◽

Cold Tolerance ◽

Genetic Basis ◽

Genome Wide Association Study ◽

Genome Wide Association ◽

Genome Wide

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Genome-wide association studies of cardiac electrical phenotypes

Cardiovascular Research ◽

10.1093/cvr/cvaa144 ◽

2020 ◽

Vol 116 (9) ◽

pp. 1620-1634

Author(s):

Charlotte Glinge ◽

Najim Lahrouchi ◽

Reza Jabbari ◽

Jacob Tfelt-Hansen ◽

Connie R Bezzina

Keyword(s):

Genetic Basis ◽

Association Studies ◽

Individual Variability ◽

Genome Wide Association ◽

Genome Wide Association Studies ◽

Nucleotide Polymorphisms ◽

Genome Wide ◽

Challenges And Opportunities ◽

Electrocardiographic Parameters

Abstract The genetic basis of cardiac electrical phenotypes has in the last 25 years been the subject of intense investigation. While in the first years, such efforts were dominated by the study of familial arrhythmia syndromes, in recent years, large consortia of investigators have successfully pursued genome-wide association studies (GWAS) for the identification of single-nucleotide polymorphisms that govern inter-individual variability in electrocardiographic parameters in the general population. We here provide a review of GWAS conducted on cardiac electrical phenotypes in the last 14 years and discuss the implications of these discoveries for our understanding of the genetic basis of disease susceptibility and variability in disease severity. Furthermore, we review functional follow-up studies that have been conducted on GWAS loci associated with cardiac electrical phenotypes and highlight the challenges and opportunities offered by such studies.

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