eQTL-seq: a Rapid Genome-Wide Integrative Genetical Genomics Strategy to Dissect Complex Regulatory Architecture of Gene Expression Underlying Quantitative Trait Variation in Crop Plants

We developed a combinatorial next generation sequencing (NGS)-based high-throughput expression QTL-seq (eQTL-seq) strategy for rapid elucidation of complex genetic architecture and regulatory pathways of gene expression underlying quantitative trait variation in crop plants. This high-resolution gen...

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Bibliographic Details
Published in:Plant molecular biology reporter 2024-06, Vol.42 (2), p.218-223
Main Authors: Mohanty, Jitendra K., Jha, Uday Chand, Dixit, G. P., Bharadwaj, Chellapilla, Parida, Swarup K.
Format: Article
Language:English
Subjects:
Alleles
Bioinformatics
Biomedical and Life Sciences
Brief Report
Chickpeas
Cloning
Combinatorial analysis
Crop improvement
Crops
Gene expression
Gene mapping
Gene polymorphism
Genes
Genetic diversity
Genomes
Genomics
High resolution
Inbreeding
Legumes
Life Sciences
Mapping
Metabolomics
Next-generation sequencing
Nucleotide sequence
Phenotypic variations
Plant breeding
Plant Breeding/Biotechnology
Plant Sciences
Polymorphism
Proteomics
Quantitative trait loci
Seeds
Single-nucleotide polymorphism
Transcription factors
Transcriptomes
Weight
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Summary:We developed a combinatorial next generation sequencing (NGS)-based high-throughput expression QTL-seq (eQTL-seq) strategy for rapid elucidation of complex genetic architecture and regulatory pathways of gene expression underlying quantitative trait variation in crop plants. This high-resolution genome-wide integrative genetical genomics strategy assists us to delineate functionally relevant molecular tags (QTLs/eQTLs, genes, master regulators/transcription factors, and alleles) regulating vital agronomic traits in order to expedite genomics-assisted breeding and crop improvement. As a proof-of-concept, the optimized eQTL-seq-led genetical genomics approach was employed in 192 mapping individuals of an intra-specific recombinant inbred line (RIL) population ( desi accession ICC 4958 ×  kabuli accession ICC 12968) with contrasting seed weight trait. This led to identification and mapping of high-resolution major QTLs/eQTLs associated with seed weight based on genome resequence-derived genomic SNP-index (Δ(gSNP-index)), global transcriptome sequence-based expression SNP-index (Δ(eSNP-index)), and relative gene expression (RGE)-index (Δ(RGE-index)). The eQTL-seq scaled down the major seed weight QTLs/eQTLs into the potential candidate gene(s) governing cis - and trans-regulated expression to decipher the gene regulatory modules controlling complex quantitative seed weight trait by deriving global allele-specific gene expression polymorphism in chickpea. Henceforth, the efficacy of NGS-driven integrative eQTL-seq strategy as compared to traditional QTL mapping, fine-mapping (map-based cloning), and QTL-seq approaches that are widely adopted for delineation of candidate genes underlying major QTLs was evident in chickpea. This will further accelerate quantitative dissection of regulatory architecture by decoding the molecular genetic basis of gene expression variation controlling diverse complex phenotypic trait diversity in chickpea and other crop plants as well.
ISSN:0735-9640
1572-9818
DOI:10.1007/s11105-023-01411-8