Interpretation of Manhattan Plots and Other Outputs of Genome-Wide Association Studies

Wang, Jiabo; Yu, Jianming; Lipka, Alexander E.; Zhang, Zhiwu

doi:10.1007/978-1-0716-2237-7_5

Cited by 4 publications

(1 citation statement)

References 88 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The genetic basis of traits like grain Fe and Zn content can be complex, involving multiple genes with small effects 24 , and this can explain the observed moderate repeatability. The observed medium to high broad-sense heritability/repeatability and wide variation within population for the evaluated micronutrients are the precondition for a successful GWAS [74][75][76] . The association between grain Fe and Zn showed significant and high positive values and the trend was similar across environments, implying that selection for either mineral can be used as proxy for the other.…”

Section: Discussionmentioning

confidence: 99%

Genome-wide association study and expression of candidate genes for Fe and Zn concentration in sorghum grains

Thakur,

Gorthy,

Vemula

et al. 2024

Sci Rep

View full text Add to dashboard Cite

Sorghum germplasm showed grain Fe and Zn genetic variability, but a few varieties were biofortified with these minerals. This work contributes to narrowing this gap. Fe and Zn concentrations along with 55,068 high-quality GBS SNP data from 140 sorghum accessions were used in this study. Both micronutrients exhibited good variability with respective ranges of 22.09–52.55 ppm and 17.92–43.16 ppm. Significant marker-trait associations were identified on chromosomes 1, 3, and 5. Two major effect SNPs (S01_72265728 and S05_58213541) explained 35% and 32% of Fe and Zn phenotypic variance, respectively. The SNP S01_72265728 was identified in the cytochrome P450 gene and showed a positive effect on Fe accumulation in the kernel, while S05_58213541 was intergenic near Sobic.005G134800 (zinc-binding ribosomal protein) and showed negative effect on Zn. Tissue-specific in silico expression analysis resulted in higher levels of Sobic.003G350800 gene product in several tissues such as leaf, root, flower, panicle, and stem. Sobic.005G188300 and Sobic.001G463800 were expressed moderately at grain maturity and anthesis in leaf, root, panicle, and seed tissues. The candidate genes expressed in leaves, stems, and grains will be targeted to improve grain and stover quality. The haplotypes identified will be useful in forward genetics breeding.

show abstract

Section: Discussionmentioning

confidence: 99%

Genome-wide association study and expression of candidate genes for Fe and Zn concentration in sorghum grains

Thakur,

Gorthy,

Vemula

et al. 2024

Sci Rep

View full text Add to dashboard Cite

show abstract

The Application of Molecular Markers in Fish Breeding and Aquaculture

Rodrigues

Biun

Yong

et al. 2023

Marine Biotechnology: Applications in Food, Drugs and Energy

View full text Add to dashboard Cite

Multiple-statistical genome-wide association analysis and genomic prediction of fruit aroma and agronomic traits in peaches

Wang

et al. 2023

Horticulture Research

View full text Add to dashboard Cite

‘Chinese Cling’ is an important founder in peach breeding history due to the pleasant flavor. Genome-wide association studies (GWAS) combined with genomic selection (GS) are promising tools in fruit tree breeding, as there is a considerable time lapse between crossing and release of a cultivar. In this study, 242 peaches from Shanghai germplasm were genotyped with 145,456 single nucleotide polymorphisms (SNPs). The six agronomic traits of fruit flesh color, fruit shape, fruit hairiness, flower type, pollen sterility, and soluble solid content, along with fourteen key volatile odor compounds (VOCs) were recorded for multiple-statistical GWAS. Except the reported candidate genes, six novel genes were identified to be associated with these traits. Thirty-nine significant SNPs were associated with eight VOCs. The putative candidate genes were confirmed for VOCs by RNA-seq, including three genes in the biosynthesis pathway found to be associated with linalool, soluble solid content and cis-3-hexenyl acetate. The multiple-traits genomic prediction enhanced the predictive ability for γ-decalactone to 0.7415 compared with the single-traits model value of 0.1017. One PTS1-SSR marker was designed to predict the linalool content, and the favorable genotype 187/187 was confirmed, mainly existing in “Shanghai Shuimi” landrace. Overall, our findings will be helpful to determine the peach accessions with the ideal phenotype and show the potential of multiple-trait genomic prediction to improve the accuracy for highly correlated genetic traits. The diagnostic marker will be valuable for the breeder to bridge the gap between QTLs and marker assisted selection (MAS) for developing strong-aroma cultivars.

show abstract

Interpretation of Manhattan Plots and Other Outputs of Genome-Wide Association Studies

Cited by 4 publications

References 88 publications

Genome-wide association study and expression of candidate genes for Fe and Zn concentration in sorghum grains

Genome-wide association study and expression of candidate genes for Fe and Zn concentration in sorghum grains

The Application of Molecular Markers in Fish Breeding and Aquaculture

Multiple-statistical genome-wide association analysis and genomic prediction of fruit aroma and agronomic traits in peaches

Contact Info

Product

Resources

About