scholarly journals Identification of Novel Genomic Regions and Superior Alleles Associated with Zn Accumulation in Wheat Using a Genome-Wide Association Analysis Method

2020 ◽  
Vol 21 (6) ◽  
pp. 1928 ◽  
Author(s):  
Zhengfu Zhou ◽  
Xia Shi ◽  
Ganqing Zhao ◽  
Maomao Qin ◽  
Maria Itria Ibba ◽  
...  
Keyword(s):  
Quantitative Trait Loci ◽  
Quantitative Trait ◽  
Genome Wide Association Study ◽  
Genome Wide Association ◽  
Zn Deficiency ◽  
Wheat Grains ◽  
Zn Accumulation ◽  
Genome Wide ◽  
A Genome ◽  
Trait Loci

Micronutrient deficiencies, and especially zinc (Zn) deficiency, pose serious health problems to people who mainly depend on cereal-based diets. Here, we performed a genome-wide association study (GWAS) to detect the genetic basis of the Zn accumulation in wheat (Triticum aestivum L.) grains with a diversity panel of 207 bread wheat varieties. To uncover authentic quantitative trait loci (QTL) controlling Zn accumulation, the varieties were planted in three locations. In total, 29 unique loci associated with Zn grain accumulation were identified. Notably, seven non-redundant loci located on chromosomes 1B, 3B, 3D, 4A, 5A, 5B, and 7A, were detected at least in two environments. Of these quantitative trait loci (QTL), six coincided with known QTL or genes, whereas the highest effect QTL on chromosome 3D identified in this study was not reported previously. Searches of public databases revealed that the seven identified QTL coincided with seven putative candidate genes linked to Zn accumulation. Among these seven genes, NAC domain-containing protein gene (TraesCS3D02G078500) linked with the most significant single nucleotide polymorphism (SNP) AX-94729264 on chromosome 3D was relevant to metal accumulation in wheat grains. Results of this study provide new insights into the genetic architecture of Zn accumulation in wheat grains.

scholarly journals A Genome-Wide Association Study Identifies Protein Quantitative Trait Loci (pQTLs)

PLoS Genetics ◽  
2008 ◽  
Vol 4 (5) ◽  
pp. e1000072 ◽  
Author(s):  
David Melzer ◽  
John R. B. Perry ◽  
Dena Hernandez ◽  
Anna-Maria Corsi ◽  
Kara Stevens ◽  
...  
Keyword(s):  
Quantitative Trait Loci ◽  
Association Study ◽  
Quantitative Trait ◽  
Genome Wide Association Study ◽  
Genome Wide Association ◽  
Genome Wide ◽  
A Genome ◽  
Trait Loci

scholarly journals Identification of Quantitative Trait Loci for Leaf Rust and Stem Rust Seedling Resistance in Bread Wheat Using a Genome-Wide Association Study

Plants ◽  
2021 ◽  
Vol 11 (1) ◽  
pp. 74
Author(s):  
Alibek Zatybekov ◽  
Yuliya Genievskaya ◽  
Aralbek Rsaliyev ◽  
Akerke Maulenbay ◽  
Gulbahar Yskakova ◽  
...  
Keyword(s):  
Quantitative Trait Loci ◽  
Association Study ◽  
Leaf Rust ◽  
Bread Wheat ◽  
Stem Rust ◽  
Quantitative Trait ◽  
Genome Wide Association Study ◽  
Genome Wide Association ◽  
Genome Wide ◽  
A Genome

In recent years, leaf rust (LR) and stem rust (SR) have become a serious threat to bread wheat production in Kazakhstan. Most local cultivars are susceptible to these rusts, which has affected their yield and quality. The development of new cultivars with high productivity and LR and SR disease resistance, including using marker-assisted selection, is becoming an important priority in local breeding projects. Therefore, the search for key genetic factors controlling resistance in all plant stages, including the seedling stage, is of great significance. In this work, we applied a genome-wide association study (GWAS) approach using 212 local bread wheat accessions that were phenotyped for resistance to specific races of Puccinia triticina Eriks. (Pt) and Puccinia graminis f. sp. tritici (Pgt) at the seedling stages. The collection was genotyped using a 20 K Illumina iSelect SNP assay, and 11,150 polymorphic SNP markers were selected for the association mapping. Using a mixed linear model, we identified 11 quantitative trait loci (QTLs) for five out of six specific races of Pt and Pgt. The comparison of the results from this GWAS with those from previously published work showed that nine out of eleven QTLs for LR and SR resistance had been previously reported in a GWAS study at the adult plant stages of wheat growth. Therefore, it was assumed that these nine common identified QTLs were effective for all-stage resistance to LR and SR, and the two other QTLs appear to be novel QTLs. In addition, five out of these nine QTLs that had been identified earlier were found to be associated with yield components, suggesting that they may directly influence the field performance of bread wheat. The identified QTLs, including novel QTLs found in this study, may play an essential role in the breeding process for improving wheat resistance to LR and SR.

scholarly journals Common Expression Quantitative Trait Loci Shared by Histone Genes

2017 ◽  
Vol 2017 ◽  
pp. 1-14
Author(s):  
Hanseol Kim ◽  
Yujin Suh ◽  
Chaeyoung Lee
Keyword(s):  
Quantitative Trait Loci ◽  
Quantitative Trait ◽  
Genome Wide Association Study ◽  
Histone Genes ◽  
Expression Quantitative Trait Loci ◽  
Nucleotide Polymorphisms ◽  
Genome Wide ◽  
A Genome ◽  
Trait Loci ◽  
Cycle Dependent

A genome-wide association study (GWAS) was conducted to examine expression quantitative trait loci (eQTLs) for histone genes. We examined common eQTLs for multiple histone genes in 373 European lymphoblastoid cell lines (LCLs). A linear regression model was employed to identify single-nucleotide polymorphisms (SNPs) associated with expression of the histone genes, and the number of eQTLs was determined by linkage disequilibrium analysis. Additional associations of the identified eQTLs with other genes were also examined. We identified 31 eQTLs for 29 histone genes through genome-wide analysis using 29 histone genes (P<2.97×10−10). Among them, 12 eQTLs were associated with the expression of multiple histone genes. Transcriptome-wide association analysis using the identified eQTLs showed their associations with additional 80 genes (P<4.75×10−6). In particular, expression of RPPH1, SCARNA2, and SCARNA7 genes was associated with 26, 25, and 23 eQTLs, respectively. This study suggests that histone genes shared 12 common eQTLs that might regulate cell cycle-dependent transcription of histone and other genes. Further investigations are needed to elucidate the transcriptional mechanisms of these genes.

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