Pinpointing genomic regions and candidate genes associated with seed oil and protein content in soybean through an integrative transcriptomic and QTL meta-analysis
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Date
2023
Journal Title
Journal ISSN
Volume Title
Publisher
Cells
Abstract
Soybean with enriched nutrients has emerged as a prominent source of edible oil and
protein. In the present study, a meta-analysis was performed by integrating quantitative trait loci
(QTLs) information, region-specific association and transcriptomic analysis. Analysis of about
a thousand QTLs previously identified in soybean helped to pinpoint 14 meta-QTLs for oil and
16 meta-QTLs for protein content. Similarly, region-specific association analysis using whole genome
re-sequenced data was performed for the most promising meta-QTL on chromosomes 6 and 20. Only
94 out of 468 genes related to fatty acid and protein metabolic pathways identified within the meta-
QTL region were found to be expressed in seeds. Allele mining and haplotyping of these selected
genes were performed using whole genome resequencing data. Interestingly, a significant haplotypic
association of some genes with oil and protein content was observed, for instance, in the case of FAD2-
1B gene, an average seed oil content of 20.22% for haplotype 1 compared to 15.52% for haplotype 5
was observed. In addition, the mutation S86F in the FAD2-1B gene produces a destabilizing effect
of (DDG Stability) 0.31 kcal/mol. Transcriptomic analysis revealed the tissue-specific expression
of candidate genes. Based on their higher expression in seed developmental stages, genes such as
sugar transporter, fatty acid desaturase (FAD), lipid transporter, major facilitator protein and amino
acid transporter can be targeted for functional validation. The approach and information generated
in the present study will be helpful in the map-based cloning of regulatory genes, as well as for
marker-assisted breeding in soybean.
Description
Keywords
haplotyping; meta-analysis; nutrition; quantitative trait loci; soybean; transcriptomics