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

Md Atik Us Saieed; Yun Zhao; Shahidul Islam; Wujun Ma

doi:10.3390/plants13010026

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

Journal article

Open access

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

Md Atik Us Saieed, Yun Zhao, Shahidul Islam and Wujun Ma

Plants (Basel), Vol.13(1), 26

2023

DOI: https://doi.org/10.3390/plants13010026

PMID: 38202333

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Abstract

gene identification

quantitative trait locus (QTL)

bioinformatics

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.

Details

Title: Identifying and Characterizing Candidate Genes Contributing to a Grain Yield QTL in Wheat
Authors/Creators: Md Atik Us Saieed - Murdoch University
Yun Zhao - Murdoch University
Shahidul Islam - Murdoch University, Centre for Crop and Food Innovation
Wujun Ma - Murdoch University, Centre for Crop and Food Innovation
Publication Details: Plants (Basel), Vol.13(1), 26
Publisher: MDPI
Grant note: UMU00048 / Grains Research and Development Corporation
Identifiers: 991005626967707891
Murdoch Affiliation: College of Health and Education; Food Futures Institute
Language: English
Resource Type: Journal article

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