Validating Genic SNPs in Chickpea

To validate genic SNPs identified between C. microphyllum and ICC 4958 in silico, the genotyping information of SNPs differentiating these two chickpea accessions was compared/correlated with the available in silico SNP database according to their nature/types of SNP alleles and physical positions (bp) on the desi (ICC 4958) genome11 (link)25 (link)26 (link)50 (link)51 (link). For experimental validation and understanding the functional significance of mined SNPs, 192 coding (including non-synonymous and large-effect substitutions) and regulatory SNPs (physically mapped on chromosomes) were selected from root-specific genes/TF-encoding genes of C. microphyllum based on their drought-responsive differential expression especially in the roots of ICC 4958. These SNPs were further genotyped in 96 wild and cultivated chickpea accessions (including known drought tolerant and sensitive accessions selected for differential expression profiling) using Sequenom MALDI-TOF (matrix-assisted laser desorption ionization-time of flight) MassARRAY as per Saxena et al.2 (link) and Bajaj et al.11 (link).

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Srivastava R., Bajaj D., Malik A., Singh M, & Parida S.K. (2016). Transcriptome landscape of perennial wild Cicer microphyllum uncovers functionally relevant molecular tags regulating agronomic traits in chickpea. Scientific Reports, 6, 33616.

Publication 2016

MALDI-TOF

Alleles Chickpea Chromosomes Drought Genes root Genic Matrix assisted laser desorption ionization Physical Roots Snps

Corresponding Organization :

Other organizations : National Institute of Plant Genome Research, Jamia Hamdard, National Bureau of Plant Genetic Resources

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Variable analysis

independent variables

Chickpea accessions (96 wild and cultivated accessions, including known drought tolerant and sensitive accessions)

dependent variables

Genotyping information of SNPs differentiating C. microphyllum and ICC 4958 chickpea accessions
Functional significance of mined SNPs

control variables

SNP database according to their nature/types of SNP alleles and physical positions (bp) on the desi (ICC 4958) genome
Sequenom MALDI-TOF (matrix-assisted laser desorption ionization-time of flight) MassARRAY genotyping technique

controls

Positive control: Not explicitly mentioned
Negative control: Not explicitly mentioned

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