title: Genome-wide development and deployment of informative intron-spanning and intron-length polymorphism markers for genomics-assisted breeding applications in chickpea.
abstract: The discovery and large-scale genotyping of informative gene-based markers is essential for rapid delineation of genes/QTLs governing stress tolerance and yield component traits in order to drive genetic enhancement in chickpea. A genome-wide 119169 and 110491 ISM (intron-spanning markers) from 23129 desi and 20386 kabuli protein-coding genes and 7454 in silico InDel (insertion-deletion) (1-45-bp)-based ILP (intron-length polymorphism) markers from 3283 genes were developed that were structurally and functionally annotated on eight chromosomes and unanchored scaffolds of chickpea. A much higher amplification efficiency (83%) and intra-specific polymorphic potential (86%) detected by these markers than that of other sequence-based genetic markers among desi and kabuli chickpea accessions was apparent even by a cost-effective agarose gel-based assay. The genome-wide physically mapped 1718 ILP markers assayed a wider level of functional genetic diversity (19-81%) and well-defined phylogenetics among domesticated chickpea accessions. The gene-derived 1424 ILP markers were anchored on a high-density (inter-marker distance: 0.65cM) desi intra-specific genetic linkage map/functional transcript map (ICC 4958×ICC 2263) of chickpea. This reference genetic map identified six major genomic regions harbouring six robust QTLs mapped on five chromosomes, which explained 11-23% seed weight trait variation (7.6-10.5 LOD) in chickpea. The integration of high-resolution QTL mapping with differential expression profiling detected six including one potential serine carboxypeptidase gene with ILP markers (linked tightly to the major seed weight QTLs) exhibiting seed-specific expression as well as pronounced up-regulation especially in seeds of high (ICC 4958) as compared to low (ICC 2263) seed weight mapping parental accessions. The marker information generated in the present study was made publicly accessible through a user-friendly web-resource, "Chickpea ISM-ILP Marker Database". The designing of multiple ISM and ILP markers (2-5 markers/gene) from an individual gene (transcription factor) with numerous aforementioned desirable genetic attributes can widen the user-preference to select suitable primer combination for simultaneous large-scale assaying of functional allelic variation, natural allelic diversity, molecular mapping and expression profiling of genes among chickpea accessions. This will essentially accelerate the identification of functionally relevant molecular tags regulating vital agronomic traits for genomics-assisted crop improvement by optimal resource expenses in chickpea.
authors.affiliation: National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India.
authors.forename: Rishi
authors.initials: R
authors.lastname: Srivastava
authors.affiliation: National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India.
authors.forename: Deepak
authors.initials: D
authors.lastname: Bajaj
authors.affiliation: Centre for Agricultural Bioinformatics, Indian Council of Agricultural Research (ICAR)-Indian Agricultural Statistics Research Institute, New Delhi 110012, India.
authors.forename: Yogesh K
authors.initials: YK
authors.lastname: Sayal
authors.affiliation: Division of Statistical Genetics, Indian Council of Agricultural Research (ICAR)-Indian Agricultural Statistics Research Institute, New Delhi 110012, India.
authors.forename: Prabina K
authors.initials: PK
authors.lastname: Meher
authors.affiliation: International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru 502324, Telangana, India.
authors.forename: Hari D
authors.initials: HD
authors.lastname: Upadhyaya
authors.affiliation: U.P. Council of Agricultural Research, Gomati Nagar, Lucknow 226010, Uttar Pradesh, India.
authors.forename: Rajendra
authors.initials: R
authors.lastname: Kumar
authors.affiliation: Division of Genetics, Indian Agricultural Research Institute (IARI), New Delhi 110012, India.
authors.forename: Shailesh
authors.initials: S
authors.lastname: Tripathi
authors.affiliation: Division of Genetics, Indian Agricultural Research Institute (IARI), New Delhi 110012, India.
authors.forename: Chellapilla
authors.initials: C
authors.lastname: Bharadwaj
authors.affiliation: Centre for Agricultural Bioinformatics, Indian Council of Agricultural Research (ICAR)-Indian Agricultural Statistics Research Institute, New Delhi 110012, India.
authors.forename: Atmakuri R
authors.initials: AR
authors.lastname: Rao
authors.affiliation: National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India. Electronic address: swarup@nipgr.ac.in.
authors.forename: Swarup K
authors.initials: SK
authors.lastname: Parida
mesh_terms: D002874:Chromosome Mapping; D029863:Cicer / Q000235:genetics* / Q000254:growth & development; D030541:Databases, Genetic; D020869:Gene Expression Profiling; D005818:Genetic Engineering / Q000379:methods; D005819:Genetic Markers; D018745:Genome, Plant; D023281:Genomics / Q000379:methods*; D060005:Genotyping Techniques; D007438:Introns; D010641:Phenotype; D000069600:Plant Breeding / Q000379:methods; D011110:Polymorphism, Genetic; D040641:Quantitative Trait Loci; D013312:Stress, Physiological / Q000235:genetics
chemical_list: D005819:Genetic Markers
keywords: Chickpea; Genetic map; ILP; ISM; Marker; QTL