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 Comprehensive Genome-Wide Association Analysis Reveals the Genetic Basis of Root System Architecture in Soybean

2020 ◽  
Vol 11 ◽  
Author(s):  
Waldiodio Seck ◽  
Davoud Torkamaneh ◽  
François Belzile
Keyword(s):  
Root System ◽  
System Architecture ◽  
Phenotypic Variation ◽  
Genetic Basis ◽  
Genome Wide Association Study ◽  
Primary Root ◽  
Root System Architecture ◽  
Genome Wide Association ◽  
Nucleotide Polymorphisms ◽  
Genome Wide

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.

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

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.

scholarly journals Common Susceptibility Loci for Male Breast Cancer

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 &lt; 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.

Genome‐wide association study identifies variants associated with hair length in Brangus cattle

2020 ◽  
Vol 51 (5) ◽  
pp. 811-814 ◽  
Author(s):  
K. M. Sarlo Davila ◽  
A. Howell ◽  
A. Nunez ◽  
A. Orelien ◽  
V. Roe ◽  
...  
Keyword(s):  
Association Study ◽  
Genome Wide Association Study ◽  
Genome Wide Association ◽  
Hair Length ◽  
Genome Wide

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

2020 ◽  
Vol 40 (4) ◽  
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

scholarly journals Genome-wide association study of biologically informed periodontal complex traits offers novel insights into the genetic basis of periodontal disease

2016 ◽  
Vol 25 (10) ◽  
pp. 2113-2129 ◽  
Author(s):  
Steven Offenbacher ◽  
Kimon Divaris ◽  
Silvana P. Barros ◽  
Kevin L. Moss ◽  
Julie T. Marchesan ◽  
...  
Keyword(s):  
Periodontal Disease ◽  
Association Study ◽  
Complex Traits ◽  
Genetic Basis ◽  
Genome Wide Association Study ◽  
Genome Wide Association ◽  
Genome Wide

scholarly journals Assessment of the Genetic Basis of Rosacea by Genome-Wide Association Study

2015 ◽  
Vol 135 (6) ◽  
pp. 1548-1555 ◽  
Author(s):  
Anne Lynn S. Chang ◽  
Inbar Raber ◽  
Jin Xu ◽  
Rui Li ◽  
Robert Spitale ◽  
...  
Keyword(s):  
Association Study ◽  
Genetic Basis ◽  
Genome Wide Association Study ◽  
Genome Wide Association ◽  
Genome Wide

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.

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