scholarly journals Identification and Functional Verification of Cold Tolerance Genes in Spring Maize Seedlings Based on a Genome-Wide Association Study and Quantitative Trait Locus Mapping

2021 ◽  
Vol 12 ◽  
Author(s):  
Yukun Jin ◽  
Zhongren Zhang ◽  
Yongjing Xi ◽  
Zhou Yang ◽  
Zhifeng Xiao ◽  
...  
Keyword(s):  
Quantitative Trait Locus ◽  
Food Security ◽  
Qtl Mapping ◽  
Cold Tolerance ◽  
Quantitative Trait ◽  
Genome Wide Association ◽  
Maize Growth ◽  
Genome Wide ◽  
A Genome ◽  
Trait Locus

Maize (Zea mays L.) is a tropical crop, and low temperature has become one of the main abiotic stresses for maize growth and development, affecting many maize growth processes. The main area of maize production in China, Jilin province, often suffers from varying degrees of cold damage in spring, which seriously affects the quality and yield of maize. In the face of global climate change and food security concerns, discovering cold tolerance genes, developing cold tolerance molecular markers, and creating cold-tolerant germplasm have become urgent for improving maize resilience against these conditions and obtaining an increase in overall yield. In this study, whole-genome sequencing and genotyping by sequencing were used to perform genome-wide association analysis (GWAS) and quantitative trait locus (QTL) mapping of the two populations, respectively. Overall, four single-nucleotide polymorphisms (SNPs) and 12 QTLs were found to be significantly associated with cold tolerance. Through joint analysis, an intersection of GWAS and QTL mapping was found on chromosome 3, on which the Zm00001d002729 gene was identified as a potential factor in cold tolerance. We verified the function of this target gene through overexpression, suppression of expression, and genetic transformation into maize. We found that Zm00001d002729 overexpression resulted in better cold tolerance in this crop. The identification of genes associated with cold tolerance contributes to the clarification of the underlying mechanism of this trait in maize and provides a foundation for the adaptation of maize to colder environments in the future, to ensure food security.

scholarly journals Epigenome-Wide Study Identified Methylation Sites Associated with the Risk of Obesity

Nutrients ◽  
2021 ◽  
Vol 13 (6) ◽  
pp. 1984
Author(s):  
Majid Nikpay ◽  
Sepehr Ravati ◽  
Robert Dent ◽  
Ruth McPherson
Keyword(s):  
Quantitative Trait Locus ◽  
Quantitative Trait ◽  
Rare Variants ◽  
Genome Wide ◽  
A Genome ◽  
Genome Wide Search ◽  
Risk Snps ◽  
Trait Locus ◽  
Genomic Regions ◽  
Eqtl Data

Here, we performed a genome-wide search for methylation sites that contribute to the risk of obesity. We integrated methylation quantitative trait locus (mQTL) data with BMI GWAS information through a SNP-based multiomics approach to identify genomic regions where mQTLs for a methylation site co-localize with obesity risk SNPs. We then tested whether the identified site contributed to BMI through Mendelian randomization. We identified multiple methylation sites causally contributing to the risk of obesity. We validated these findings through a replication stage. By integrating expression quantitative trait locus (eQTL) data, we noted that lower methylation at cg21178254 site upstream of CCNL1 contributes to obesity by increasing the expression of this gene. Higher methylation at cg02814054 increases the risk of obesity by lowering the expression of MAST3, whereas lower methylation at cg06028605 contributes to obesity by decreasing the expression of SLC5A11. Finally, we noted that rare variants within 2p23.3 impact obesity by making the cg01884057 site more susceptible to methylation, which consequently lowers the expression of POMC, ADCY3 and DNAJC27. In this study, we identify methylation sites associated with the risk of obesity and reveal the mechanism whereby a number of these sites exert their effects. This study provides a framework to perform an omics-wide association study for a phenotype and to understand the mechanism whereby a rare variant causes a disease.

Complete and overlapping congenics proving the existence of a quantitative trait locus for blood pressure on Dahl rat chromosome 17

2005 ◽  
Vol 21 (1) ◽  
pp. 112-116 ◽  
Author(s):  
Myrian Grondin ◽  
Vasiliki Eliopoulos ◽  
Raphaelle Lambert ◽  
Yishu Deng ◽  
Anita Ariyarajah ◽  
...  
Keyword(s):  
Blood Pressure ◽  
Quantitative Trait Locus ◽  
Quantitative Trait ◽  
Congenic Strain ◽  
Chromosome 17 ◽  
Congenic Strains ◽  
Genome Wide ◽  
A Genome ◽  
Trait Locus ◽  
Negative Controls

Linkage studies suggested that a quantitative trait locus (QTL) for blood pressure (BP) was present in a region on chromosome 17 (Chr 17) of Dahl salt-sensitive (DSS) rats. A subsequent congenic strain targeting this QTL, however, could not confirm it. These conflicting results called into question the validity of localization of a QTL by linkage followed by the use of a congenic strain made with an incomplete chromosome coverage. To resolve this issue, we constructed five new congenic strains, designated C17S.L1 to C17S.L5, that completely spanned the ±2 LOD confidence interval supposedly containing the QTL. Each congenic strain was made by replacing a segment of the DSS rat by that of the normotensive Lewis (LEW) rat. The only section to be LL homozygous is the region on Chr 17 specified in a congenic strain, as evidenced by a total genome scan. The results showed that BPs of C17S.L1 and C17S.L2 were lower ( P < 0.04) than that of DSS rats. In contrast, BPs of C17S.L3, C17S.L4, and C17S.L5 were not different ( P > 0.6) from that of DSS rats. Consequently, a BP QTL must be located in an interval of ∼15 cM shared between C17S.L1 and C17S.L2 and unique to them both, as opposed to C17S.L3, C17S.L4, and C17S.L5. The present study illustrates the importance of thorough chromosome coverage, the necessity for a genome-wide screening, and the use of “negative” controls in physically mapping a QTL by congenic strains.

A quantitative trait locus influencing estrogen levels maps to a region homologous to human chromosome 20

2001 ◽  
Vol 5 (2) ◽  
pp. 75-80 ◽  
Author(s):  
LISA J. MARTIN ◽  
JOHN BLANGERO ◽  
JEFFREY ROGERS ◽  
MICHAEL C. MAHANEY ◽  
JAMES E. HIXSON ◽  
...  
Keyword(s):  
Quantitative Trait Locus ◽  
Human Chromosome ◽  
Quantitative Trait ◽  
Potential Candidate ◽  
General Pedigree ◽  
Genome Wide ◽  
A Genome ◽  
Component Approach ◽  
Trait Locus ◽  
Variance Component Approach

Estrogen, a steroid hormone, regulates reproduction and has been implicated in several diseases. We performed a genome-wide scan using multipoint linkage analysis implemented in a general pedigree-based variance component approach to identify genes with measurable effects on variation in estrogen levels in baboons. A microsatellite polymorphism, D20S171, located on human chromosome 20q13.11, showed strong evidence of linkage with a LOD score of 3.06 ( P = 0.00009). This region contains several potential candidate genes including melanocortin 3 receptor ( MC3R), cytochrome P-450 subfamily XXIV ( CYP24), and breast carcinoma amplified sequence ( BCAS1). This is the first evidence of a quantitative trait locus with a significant effect on estrogen.

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