Deploying QTL-seq for rapid delineation of a potential candidate gene underlying major trait-associated QTL in chickpea
| Autor: | Deepak Bajaj, Sube Singh, C. L. Laxmipathi Gowda, Swarup K. Parida, Shailesh Tripathi, Alice Kujur, Hari D. Upadhyaya, Shivali Sharma, Shouvik Das, Vinod Kumar, Saurabh Badoni, Laxmi, Akhilesh K. Tyagi |
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| Rok vydání: | 2014 |
| Předmět: |
Candidate gene
Genotype Genetic Linkage QTL Population Quantitative Trait Loci SNP Locus (genetics) Quantitative trait locus Biology Polymorphism Single Nucleotide Chromosomes Plant Family-based QTL mapping Genetic linkage chickpea Genetics education Molecular Biology Gene Plant Proteins education.field_of_study food and beverages Chromosome Mapping General Medicine Full Papers Cicer NGS QTL-seq Seeds Microsatellite Repeats |
| Zdroj: | DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes |
| ISSN: | 1756-1663 |
| Popis: | A rapid high-resolution genome-wide strategy for molecular mapping of major QTL(s)/gene(s) regulating important agronomic traits is vital for in-depth dissection of complex quantitative traits and genetic enhancement in chickpea. The present study for the first time employed a NGS-based whole-genome QTL-seq strategy to identify one major genomic region harbouring a robust 100-seed weight QTL using an intra-specific 221 chickpea mapping population (desi cv. ICC 7184 × desi cv. ICC 15061). The QTL-seq-derived major SW QTL (CaqSW1.1) was further validated by single-nucleotide polymorphism (SNP) and simple sequence repeat (SSR) marker-based traditional QTL mapping (47.6% R2 at higher LOD >19). This reflects the reliability and efficacy of QTL-seq as a strategy for rapid genome-wide scanning and fine mapping of major trait regulatory QTLs in chickpea. The use of QTL-seq and classical QTL mapping in combination narrowed down the 1.37 Mb (comprising 177 genes) major SW QTL (CaqSW1.1) region into a 35 kb genomic interval on desi chickpea chromosome 1 containing six genes. One coding SNP (G/A)-carrying constitutive photomorphogenic9 (COP9) signalosome complex subunit 8 (CSN8) gene of these exhibited seed-specific expression, including pronounced differential up-/down-regulation in low and high seed weight mapping parents and homozygous individuals during seed development. The coding SNP mined in this potential seed weight-governing candidate CSN8 gene was found to be present exclusively in all cultivated species/genotypes, but not in any wild species/genotypes of primary, secondary and tertiary gene pools. This indicates the effect of strong artificial and/or natural selection pressure on target SW locus during chickpea domestication. The proposed QTL-seq-driven integrated genome-wide strategy has potential to delineate major candidate gene(s) harbouring a robust trait regulatory QTL rapidly with optimal use of resources. This will further assist us to extrapolate the molecular mechanism underlying complex quantitative traits at a genome-wide scale leading to fast-paced marker-assisted genetic improvement in diverse crop plants, including chickpea. |
| Databáze: | OpenAIRE |
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