Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2023 Dec 20;13(1):26.
doi: 10.3390/plants13010026.

Identifying and Characterizing Candidate Genes Contributing to a Grain Yield QTL in Wheat

Md Atik Us Saieed  1   2 , Yun Zhao  1 , Shahidul Islam  1   3 , Wujun Ma  1   4
Affiliations

Identifying and Characterizing Candidate Genes Contributing to a Grain Yield QTL in Wheat

Md Atik Us Saieed et al. Plants (Basel). .

Abstract

The current study focuses on identifying the candidate genes of a grain yield QTL from a double haploid population, Westonia × Kauz. The QTL region spans 20 Mbp on the IWGSC whole-genome sequence flank with 90K SNP markers. The IWGSC gene annotation revealed 16 high-confidence genes and 41 low-confidence genes. Bioinformatic approaches, including functional gene annotation, ontology investigation, pathway exploration, and gene network study using publicly available gene expression data, enabled the short-listing of four genes for further confirmation. Complete sequencing of those four genes demonstrated that only two genes are polymorphic between the parental cultivars, which are the ferredoxin-like protein gene and the tetratricopeptide-repeat (TPR) protein gene. The two genes were selected for downstream investigation. Two SNP variations were observed in the exon for both genes, with one SNP resulting in changes in amino acid sequence. qPCR-based gene expression showed that both genes were highly expressed in the high-yielding double haploid lines along with the parental cultivar Westonia. In contrast, their expression was significantly lower in the low-yielding lines in the other parent. It can be concluded that these two genes are the contributing genes to the grain yield QTL.

Keywords: bioinformatics; gene identification; quantitative trait locus (QTL).

PubMed Disclaimer

Conflict of interest statement

The authors declare no conflict of interest.

Figures

Figure 1
Figure 1
Level of expression of the HC genes obtained from Wheat Expression Browser (expVIP).
Figure 2
Figure 2
Gene structure and SNP detection followed by comparing the resultant amino acids for the selected genes of the parental cultivars Westonia and Kauz.
Figure 3
Figure 3
Expression of ferredoxin gene (TraesCS1B02G337100) in high and low-yielding lines. The vertical bar indicates the standard error.
Figure 4
Figure 4
Expression of the tetratricopeptide-repeat gene (TraesCS1B02G337400) in high and low-yielding lines. The vertical bar indicates the standard error.
Figure 5
Figure 5
Flow diagram of the methodology for identifying candidate gene.
See this image and copyright information in PMC

Similar articles

See all similar articles

References

    1. Abdurakhmonov I.Y. Bioinformatics: Basics, Development, and Future. IntechOpen; London, UK: 2016. Bioinformatics—Updated features and applications. - DOI
    1. Adamski N.M., Borrill P., Brinton J., Harrington S.A., Marchal C., Bentley A.R., Bovill W.D., Cattivelli L., Cockram J., Moreira B.C., et al. eLife. Volume 9. eLife Sciences Publications Ltd.; Cambridge, UK: 2020. A roadmap for gene functional characterisation in crops with large genomes: Lessons from polyploid wheat. - DOI - PMC - PubMed
    1. An D., Su J., Liu Q., Zhu Y., Tong Y., Li J., Jing R., Li B., Li Z. Mapping QTLs for nitrogen uptake in relation to the early growth of wheat (Triticum aestivum L.) Plant Soil. 2006;284:73–84. doi: 10.1007/s11104-006-0030-3. - DOI
    1. Anderson W.B., Stadtman E.R. Glutamine synthetase deadenylation: A phosphorolytic reaction yielding ADP as nucleotide product. Biochem. Biophys. Res. Commun. 1970;41:704–709. doi: 10.1016/0006-291X(70)90070-7. - DOI - PubMed
    1. Appels R., Eversole K., Feuillet C., Keller B., Rogers J., Stein N., Pozniak C.J., Stein N., Choulet F., Distelfeld A., et al. Shifting the limits in wheat research and breeding using a fully annotated reference genome. Science. 2018;361:eaar7191. doi: 10.1126/science.aar7191. - DOI - PubMed

LinkOut - more resources