High-Throughput SNP Discovery and Genotyping for Constructing a Saturated Linkage Map of Chickpea (Cicer arietinum L.)

Abstract

The present study reports the large-scale discovery of genome-wide single-nucleotide polymorphisms (SNPs) in chickpea, identified mainly through the next generation sequencing of two genotypes, i.e. Cicer arietinum ICC4958 and its wild progenitor C. reticulatum PI489777, parents of an inter-specific reference mapping population of chickpea. Development and validation of a high-throughput SNP genotyping assay based on Illumina's GoldenGate Genotyping Technology and its application in building a high-resolution genetic linkage map of chickpea is described for the first time. In this study, 1022 SNPs were identified, of which 768 high-confidence SNPs were selected for designing the custom Oligo Pool All (CpOPA-I) for genotyping. Of these, 697 SNPs could be successfully used for genotyping, demonstrating a high success rate of 90.75%. Genotyping data of the 697 SNPs were compiled along with those of 368 co-dominant markers mapped in an earlier study, and a saturated genetic linkage map of chickpea was constructed. One thousand and sixty-three markers were mapped onto eight linkage groups spanning 1808.7 cM (centiMorgans) with an average inter-marker distance of 1.70 cM, thereby representing one of the most advanced maps of chickpea. The map was used for the synteny analysis of chickpea, which revealed a higher degree of synteny with the phylogenetically close Medicago than with soybean. The first set of validated SNPs and map resources developed in this study will not only facilitate QTL mapping, genome-wide association analysis and comparative mapping in legumes but also help anchor scaffolds arising out of the whole-genome sequencing of chickpea.

A SNP-Based Genetic Linkage Map of Soybean Using the SoyS - NP6K Illumina Infinium BeadChip Genotyping Array

“…SNPs are now projected to become the most useful of genetic markers, especially for the construction of dense maps (Gaur et al, 2012). The distinguished feature of the genetic linkage map presented here is that, it has been assembled based on a single population utilizing segregation data of each of the SNP markers.…”

“…However, these maps are not comparable to the map reported here as they were composed from multiple marker types and several populations. In order to increase the number of markers in a particular genome of plants and animals, the consensus maps were computed, but the maps may have lacked in accuracy of the marker order (Gaur et al, 2012). Hence, the current map of this study may be considered more accurate regarding the marker order since the markers were distributed on the linkage groups based on recombination frequencies.…”

“…Currently, various types of molecular markers are abundantly using to increase gene discovery and marker assisted selection. Among these molecular markers, single nucleotide polymorphisms (SNPs) represent the most suitable because they occurred at high density within genomes (Gaur et al, 2012). Millions of SNPs were generated in Soybean (Lam et al, 2010), Arabidopsis , Rice (Subbaiyan et al, 2012;Xu et al, 2012), and other crops (Sim et al, 2012a,b;Sharpe et al, 2013;Delourme et al, 2013).…”

Omics Study for Abiotic Stress Responses in Plants

“…Recently, transcriptome analysis by next generation sequencing (NGS), RNA-seq for sRNAs and their use in genOmics research, have greatly improved plant genomic resources. [20][21][22][23][24][25] Li et al, 26 identified 5365 differentially expressed probe sets (2-fold as cutoff) in the switch grass cultivar Alamo, under heat stress, utilizing switch grass Affy metrix gene chips. By comparative transcriptome analysis in response to heat stress, they identified 16 common genes in four monocots-switch grass, rice, wheat and maize.…”

Analysis of the Chickpea genome using next generation sequencing data

“…The high frequency of SNPs compared to SSR markers makes SNPs the marker of choice (Gaur et al, 2012 Genetic variations leading to duplication, polyploidy and gene loss (canola, blackleg fungus (Golicz et al, 2015), wheat (Gornicki et al, 1997)) are very common in the evolution of plants. Legumes of the large Papilionoideae subfamily have undergone whole genome duplication (Cannon et al, 2006).…”