ArticleScientific reports2015
A genome-wide SNP scan accelerates trait-regulatory genomic loci identification in chickpea.
Article in Scientific reports, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 51 papers, 1 of them a synthesis that pooled it.
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Who cites it
51 citing papers in PubMed, 1 synthesis or guideline pooled it, 84 citations in OpenAlex.
- Meta QTL analysis for dissecting abiotic stress tolerance in chickpea.BMC genomics · 2024Pooled it
- Trans-QTL Alliance of HKT1 and PHL7 Modulate Salinity Stress Tolerance and Enhance Crop Yield Endurance.Plant biotechnology journal · 2026Article
- A genome-wide association analysis identifies a key candidate gene controlling plant growth habit in chickpea.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2026Article
- Multi-model genome-wide association analysis of agronomic traits in a Kabuli chickpea MAGIC-subset population (Frontiers in plant science · 2026Article
- GWAS for QTLs associated with agronomic traits in Chickpea (Cicer arietinum L.) harvested in South-East Kazakhstan.BMC plant biology · 2025Article
- Haplotypes of ATP-Binding CassetteBiomolecules · 2024Article
- Zinc finger knuckle genes are associated with tolerance to drought and dehydration in chickpea (Frontiers in plant science · 2024Article
- Genome-wide association mapping identifies novel SNPs for root nodulation and agronomic traits in chickpea.Frontiers in plant science · 2024Article
- Fatty acid composition and genome-wide associations of a chickpea (Cicer arietinum L.) diversity panel for biofortification efforts.Scientific reports · 2023Article
- A superior gene allele involved in abscisic acid signaling enhances drought tolerance and yield in chickpea.Plant physiology · 2023Article
- Genetic dissection of thousand-seed weight in linseed (Frontiers in plant science · 2023Article
- Genome-wide association study as a powerful tool for dissecting competitive traits in legumes.Frontiers in plant science · 2023Review
- Integration of genome-wide association studies, metabolomics, and transcriptomics reveals phenolic acid- and flavonoid-associated genes and their regulatory elements under drought stress in rapeseed flowers.Frontiers in plant science · 2023Article
- Genome wide association analysis for grain micronutrients and anti-nutritional traits in mungbean [Frontiers in nutrition · 2023Article
- Article
- Identification of QTNs Associated With Flowering Time, Maturity, and Plant Height Traits inFrontiers in genetics · 2022Article
- Identifying Anti-Oxidant Biosynthesis Genes in Pearl Millet [Frontiers in plant science · 2021Article
- Genetic variability and population structure of Ethiopian chickpea (Cicer arietinum L.) germplasm.PloS one · 2021Article
- Evolutionary Genomics of Plant Gametophytic Selection.Plant communications · 2020Review
- Genome-wide association study for phosphate deficiency responsive root hair elongation in chickpea.Functional & integrative genomics · 2020Article
Corrections and comments
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Authors and funding
15 authors at 5 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
We identified 44844 high-quality SNPs by sequencing 92 diverse chickpea accessions belonging to a seed and pod trait-specific association panel using reference genome- and de novo-based GBS (genotyping-by-sequencing) assays. A GWAS (genome-wide association study) in an association panel of 211, including the 92 sequenced accessions, identified 22 major genomic loci showing significant association (explaining 23-47% phenotypic variation) with pod and seed number/plant and 100-seed weight. Eighteen trait-regulatory major genomic loci underlying 13 robust QTLs were validated and mapped on an intra-specific genetic linkage map by QTL mapping. A combinatorial approach of GWAS, QTL mapping and gene haplotype-specific LD mapping and transcript profiling uncovered one superior haplotype and favourable natural allelic variants in the upstream regulatory region of a CesA-type cellulose synthase (Ca_Kabuli_CesA3) gene regulating high pod and seed number/plant (explaining 47% phenotypic variation) in chickpea. The up-regulation of this superior gene haplotype correlated with increased transcript expression of Ca_Kabuli_CesA3 gene in the pollen and pod of high pod/seed number accession, resulting in higher cellulose accumulation for normal pollen and pollen tube growth. A rapid combinatorial genome-wide SNP genotyping-based approach has potential to dissect complex quantitative agronomic traits and delineate trait-regulatory genomic loci (candidate genes) for genetic enhancement in crop plants, including chickpea.
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