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

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.

[1]  J. Poulain,et al.  The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla , 2007, Nature.

[2]  Ching Yu Austin Huang,et al.  SNPstream UHT: ultra-high throughput SNP genotyping for pharmacogenomics and drug discovery. , 2002, BioTechniques.

[3]  N. Sethy,et al.  Isolation and characterization of sequence‐tagged microsatellite sites markers in chickpea (Cicer arietinum L.) , 2003 .

[4]  Matthieu G. Conte,et al.  Phylogenomics of plant genomes: a methodology for genome-wide searches for orthologs in plants , 2008, BMC Genomics.

[5]  Qifa Zhang,et al.  Genome-wide association studies of 14 agronomic traits in rice landraces , 2010, Nature Genetics.

[6]  F. Gagnon,et al.  Enhancing genetic mapping of complex genomes through the design of highly-multiplexed SNP arrays: application to the large and unsequenced genomes of white spruce and black spruce , 2008, BMC Genomics.

[7]  R. Shoemaker,et al.  High-throughput genotyping with the GoldenGate assay in the complex genome of soybean , 2008, Theoretical and Applied Genetics.

[8]  K. Chase,et al.  A Soybean Transcript Map: Gene Distribution, Haplotype and Single-Nucleotide Polymorphism Analysis , 2007, Genetics.

[9]  R. Van der Hoeven,et al.  A high density genetic map of tobacco (Nicotiana tabacum L.) obtained from large scale microsatellite marker development , 2011, Theoretical and Applied Genetics.

[10]  N. Sethy,et al.  Development of SSR and gene-targeted markers for construction of a framework linkage map of Catharanthus roseus. , 2011, Annals of botany.

[11]  S. Udupa,et al.  Characterization and mapping of sequence-tagged microsatellite sites in the chickpea (Cicer arietinum L.) genome , 1999, Molecular and General Genetics MGG.

[12]  S. Cannon,et al.  An analysis of synteny of Arachis with Lotus and Medicago sheds new light on the structure, stability and evolution of legume genomes , 2009, BMC Genomics.

[13]  Steven B Cannon,et al.  High-throughput SNP discovery through deep resequencing of a reduced representation library to anchor and orient scaffolds in the soybean whole genome sequence , 2010, BMC Genomics.

[14]  Mark H. Wright,et al.  Large‐Scale Discovery of Gene‐Enriched SNPs , 2009 .

[15]  B. Roe,et al.  Estimating genome conservation between crop and model legume species. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[16]  R. Elston,et al.  Comparison of microsatellites, single-nucleotide polymorphisms (SNPs) and composite markers derived from SNPs in linkage analysis , 2005, BMC Genetics.

[17]  John M. Burke,et al.  SNP Discovery and Development of a High-Density Genotyping Array for Sunflower , 2012, PloS one.

[18]  T. Shah,et al.  High-throughput SNP genotyping with the GoldenGate assay in maize , 2010, Molecular Breeding.

[19]  T. Huguet,et al.  Cross-species amplification of Medicago truncatula microsatellites across three major pulse crops , 2005, Theoretical and Applied Genetics.

[20]  J. Borevitz,et al.  Global Analysis of Allele-Specific Expression in Arabidopsis thaliana , 2009, Genetics.

[21]  C. Külheim,et al.  Comparative SNP diversity among four Eucalyptus species for genes from secondary metabolite biosynthetic pathways , 2009, BMC Genomics.

[22]  S. Tabata,et al.  High-density Integrated Linkage Map Based on SSR Markers in Soybean , 2009, DNA research : an international journal for rapid publication of reports on genes and genomes.

[23]  J. Crouch,et al.  Development of ESTs from chickpea roots and their use in diversity analysis of the Cicer genus , 2005, BMC Plant Biology.

[24]  Roger E Bumgarner,et al.  The genome of the domesticated apple (Malus × domestica Borkh.) , 2010, Nature Genetics.

[25]  Mukesh Jain,et al.  Gene Discovery and Tissue-Specific Transcriptome Analysis in Chickpea with Massively Parallel Pyrosequencing and Web Resource Development1[W][OA] , 2011, Plant Physiology.

[26]  T. Nishio,et al.  Extensive Chromosome Homoeology among Brassiceae Species Were Revealed by Comparative Genetic Mapping with High-Density EST-Based SNP Markers in Radish (Raphanus sativus L.) , 2011, DNA research : an international journal for rapid publication of reports on genes and genomes.

[27]  R. Malmberg.  Molecular biology of plants , 1985 .

[28]  P. Langridge,et al.  A high density barley microsatellite consensus map with 775 SSR loci , 2007, Theoretical and Applied Genetics.

[29]  C. Nusbaum,et al.  Large-scale identification, mapping, and genotyping of single-nucleotide polymorphisms in the human genome. , 1998, Science.

[30]  T. Close,et al.  A SNP and SSR Based Genetic Map of Asparagus Bean (Vigna. unguiculata ssp. sesquipedialis) and Comparison with the Broader Species , 2011, PloS one.

[31]  Bo Wang,et al.  Resequencing of 31 wild and cultivated soybean genomes identifies patterns of genetic diversity and selection , 2010, Nature Genetics.

[32]  C. Scheuring,et al.  Construction of BAC and BIBAC libraries and their applications for generation of SSR markers for genome analysis of chickpea, Cicer arietinum L. , 2005, Theoretical and Applied Genetics.

[33]  Rajeev K. Varshney,et al.  Integration of novel SSR and gene-based SNP marker loci in the chickpea genetic map and establishment of new anchor points with Medicago truncatula genome , 2010, Theoretical and Applied Genetics.

[34]  S. Chakraborty,et al.  Comparative analyses of genotype dependent expressed sequence tags and stress-responsive transcriptome of chickpea wilt illustrate predicted and unexpected genes and novel regulators of plant immunity , 2009, BMC Genomics.

[35]  K. Takeda,et al.  An application of high-throughput SNP genotyping for barley genome mapping and characterization of recombinant chromosome substitution lines , 2009, Theoretical and Applied Genetics.

[36]  T. Shah,et al.  Development and use of genic molecular markers (GMMs) for construction of a transcript map of chickpea (Cicer arietinum L.) , 2011, Theoretical and Applied Genetics.

[37]  A. Syvänen.  Toward genome-wide SNP genotyping , 2005, Nature Genetics.

[38]  R. Henry,et al.  Genome-wide DNA polymorphisms in elite indica rice inbreds discovered by whole-genome sequencing. , 2012, Plant biotechnology journal.

[39]  S. Myles,et al.  Rapid Genomic Characterization of the Genus Vitis , 2010, PloS one.

[40]  G. Kahl,et al.  Sequence-tagged microsatellite site markers for chickpea (Cicer arietinum L.). , 1999, Genome.

[41]  Bjarni J. Vilhjálmsson,et al.  Genome-wide association study of 107 phenotypes in Arabidopsis thaliana inbred lines , 2010 .

[42]  D. D. Kosambi.  The estimation of map distances from recombination values. , 1943 .

[43]  Jing Huang,et al.  Parallel genotyping of over 10,000 SNPs using a one-primer assay on a high-density oligonucleotide array. , 2004, Genome research.

[44]  P. Rouzé,et al.  Title Development and implementation of a highly-multiplexed SNP array for genetic mapping in maritime pine and comparative mapping with loblolly pine , 2011 .

[45]  A. Oliphant,et al.  BeadArray technology: enabling an accurate, cost-effective approach to high-throughput genotyping. , 2002, BioTechniques.

[46]  Jörg Schmidtke,et al.  An estimate of unique DNA sequence heterozygosity in the human genome , 2004, Human Genetics.

[47]  R. Gwilliam,et al.  Transcript-specific, single-nucleotide polymorphism discovery and linkage analysis in hexaploid bread wheat (Triticum aestivum L.). , 2011, Plant biotechnology journal.

[48]  S. Cannon,et al.  Large-scale transcriptome analysis in chickpea (Cicer arietinum L.), an orphan legume crop of the semi-arid tropics of Asia and Africa , 2011, Plant biotechnology journal.

[49]  Lin Fang,et al.  Resequencing 50 accessions of cultivated and wild rice yields markers for identifying agronomically important genes , 2011, Nature Biotechnology.

[50]  Timothy J. Close,et al.  A consensus genetic map of cowpea [Vigna unguiculata (L) Walp.] and synteny based on EST-derived SNPs , 2009, Proceedings of the National Academy of Sciences.

[51]  Stefano Lonardi,et al.  Development and implementation of high-throughput SNP genotyping in barley , 2009, BMC Genomics.

[52]  N. Sethy,et al.  Advancing the STMS genomic resources for defining new locations on the intraspecific genetic linkage map of chickpea (Cicer arietinum L.) , 2011, BMC Genomics.

[53]  G. Kahl,et al.  A linkage map of the chickpea (Cicer arietinum L.) genome based on recombinant inbred lines from a C. arietinum×C. reticulatum cross: localization of resistance genes for fusarium wilt races 4 and 5 , 2000, Theoretical and Applied Genetics.

[54]  M. McMullen,et al.  Development of single nucleotide polymorphism (SNP) markers for use in commercial maize (Zea mays L.) germplasm , 2009, Molecular Breeding.

[55]  Roeland E. Voorrips,et al.  Software for the calculation of genetic linkage maps , 2001 .

[56]  Yi Ren,et al.  A High Resolution Genetic Map Anchoring Scaffolds of the Sequenced Watermelon Genome , 2012, PloS one.

[57]  S. Tabata,et al.  An interspecific linkage map of SSR and intronic polymorphism markers in tomato , 2010, Theoretical and Applied Genetics.

[58]  K. Edwards,et al.  Development of microsatellite markers and analysis of intraspecific genetic variability in chickpea (Cicer arietinum L.) , 2006, Theoretical and Applied Genetics.

[59]  Gunnar Rätsch,et al.  Detecting polymorphic regions in Arabidopsis thaliana with resequencing microarrays. , 2008, Genome research.

[60]  I. Sussex,et al.  Molecular biology of plants : a laboratory course manual , 1985 .

[61]  M. Krawczak.  Informativity assessment for biallelic single nucleotide polymorphisms , 1999, Electrophoresis.

[62]  E. Pang,et al.  Isolation and analysis of candidate ascochyta blight defence genes in chickpea. Part I. Generation and analysis of an expressed sequence tag (EST) library , 2005 .

[63]  Mark H. Wright,et al.  High-throughput genotyping and mapping of single nucleotide polymorphisms in loblolly pine (Pinus taeda L.) , 2008, Tree Genetics & Genomes.

[64]  Kevin L. Gunderson,et al.  Highly parallel genomic assays , 2006, Nature Reviews Genetics.

[65]  Yasukazu Nakamura,et al.  SNP Discovery and Linkage Map Construction in Cultivated Tomato , 2010, DNA research : an international journal for rapid publication of reports on genes and genomes.

[66]  Bruno Marco de Lima,et al.  High-throughput SNP genotyping in the highly heterozygous genome of Eucalyptus: assay success, polymorphism and transferability across species , 2011, BMC Plant Biology.

[67]  N. Young,et al.  Whole-genome nucleotide diversity, recombination, and linkage disequilibrium in the model legume Medicago truncatula , 2011, Proceedings of the National Academy of Sciences.

[68]  M. Yano,et al.  Fine definition of the pedigree haplotypes of closely related rice cultivars by means of genome-wide discovery of single-nucleotide polymorphisms , 2010, BMC Genomics.

[69]  Akhilesh K. Tyagi,et al.  De Novo Assembly of Chickpea Transcriptome Using Short Reads for Gene Discovery and Marker Identification , 2011, DNA research : an international journal for rapid publication of reports on genes and genomes.

[70]  M. Blair,et al.  Saturation of an Intra-Gene Pool Linkage Map: Towards a Unified Consensus Linkage Map for Fine Mapping and Synteny Analysis in Common Bean , 2011, PloS one.

[71]  S. P. Fodor,et al.  Genotyping over 100,000 SNPs on a pair of oligonucleotide arrays , 2004, Nature Methods.

[72]  M. Yano,et al.  Discovery of Genome-Wide DNA Polymorphisms in a Landrace Cultivar of Japonica Rice by Whole-Genome Sequencing , 2011, Plant & cell physiology.

[73]  P. Winter,et al.  A consensus genetic map of chickpea (Cicer arietinum L.) based on 10 mapping populations , 2010, Euphytica.

[74]  Peter J. Bradbury,et al.  Genome-wide association study of leaf architecture in the maize nested association mapping population , 2011, Nature Genetics.

[75]  T. Joshi,et al.  SNP discovery by high-throughput sequencing in soybean , 2010, BMC Genomics.

[76]  Cécile Donnadieu,et al.  Highly-multiplexed SNP genotyping for genetic mapping and germplasm diversity studies in pea , 2010, BMC Genomics.

[77]  James R. Knight,et al.  Genome sequencing in microfabricated high-density picolitre reactors , 2005, Nature.

[78]  N. Sethy,et al.  Development of sequence-tagged microsatellite site markers for chickpea ( Cicer arietinum L.) , 2006 .

[79]  M T Clegg,et al.  Genome comparisons reveal a dominant mechanism of chromosome number reduction in grasses and accelerated genome evolution in Triticeae , 2009, Proceedings of the National Academy of Sciences.

[80]  Christopher D Town,et al.  A comprehensive resource of drought- and salinity- responsive ESTs for gene discovery and marker development in chickpea (Cicer arietinum L.) , 2009, BMC Genomics.

[81]  N. Sethy,et al.  Development of chickpea EST-SSR markers and analysis of allelic variation across related species , 2009, Theoretical and Applied Genetics.

[82]  C. Mézard,et al.  Meiosis : recombination and the control of cell division , 2013 .

[83]  D Bentley,et al.  Highly parallel SNP genotyping. , 2003, Cold Spring Harbor symposia on quantitative biology.

[84]  E. D. Earle,et al.  Nuclear DNA content of some important plant species , 1991, Plant Molecular Biology Reporter.

[85]  M. Luo,et al.  Comparison of a high-density genetic linkage map to genome features in the model grass Brachypodium distachyon , 2011, Theoretical and Applied Genetics.

[86]  Rajeev K. Varshney,et al.  Recent history of artificial outcrossing facilitates whole-genome association mapping in elite inbred crop varieties , 2006, Proceedings of the National Academy of Sciences.

[87]  Dustin A. Cartwright,et al.  A Dense Single-Nucleotide Polymorphism-Based Genetic Linkage Map of Grapevine (Vitis vinifera L.) Anchoring Pinot Noir Bacterial Artificial Chromosome Contigs , 2007, Genetics.

[88]  Asan,et al.  The genome of the cucumber, Cucumis sativus L. , 2009, Nature Genetics.

[89]  C. Town,et al.  Genome-wide SNP discovery in tetraploid alfalfa using 454 sequencing and high resolution melting analysis , 2011, BMC Genomics.

[90]  K. Mochida,et al.  SSR-based linkage map with new markers using an intraspecific population of common wheat , 2006, Theoretical and Applied Genetics.

[91]  R. Gaur,et al.  EST-derived genic molecular markers: development and utilization for generating an advanced transcript map of chickpea , 2012, Theoretical and Applied Genetics.