title: Genome-wide conserved non-coding microsatellite (CNMS) marker-based integrative genetical genomics for quantitative dissection of seed weight in chickpea.
abstract: Phylogenetic footprinting identified 666 genome-wide paralogous and orthologous CNMS (conserved non-coding microsatellite) markers from 5'-untranslated and regulatory regions (URRs) of 603 protein-coding chickpea genes. The (CT)n and (GA)n CNMS carrying CTRMCAMV35S and GAGA8BKN3 regulatory elements, respectively, are abundant in the chickpea genome. The mapped genic CNMS markers with robust amplification efficiencies (94.7%) detected higher intraspecific polymorphic potential (37.6%) among genotypes, implying their immense utility in chickpea breeding and genetic analyses. Seventeen differentially expressed CNMS marker-associated genes showing strong preferential and seed tissue/developmental stage-specific expression in contrasting genotypes were selected to narrow down the gene targets underlying seed weight quantitative trait loci (QTLs)/eQTLs (expression QTLs) through integrative genetical genomics. The integration of transcript profiling with seed weight QTL/eQTL mapping, molecular haplotyping, and association analyses identified potential molecular tags (GAGA8BKN3 and RAV1AAT regulatory elements and alleles/haplotypes) in the LOB-domain-containing protein- and KANADI protein-encoding transcription factor genes controlling the cis-regulated expression for seed weight in the chickpea. This emphasizes the potential of CNMS marker-based integrative genetical genomics for the quantitative genetic dissection of complex seed weight in chickpea.
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: National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India.
authors.forename: Maneesha S
authors.initials: MS
authors.lastname: Saxena
authors.affiliation: National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India.
authors.forename: Alice
authors.initials: A
authors.lastname: Kujur
authors.affiliation: National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India.
authors.forename: Shouvik
authors.initials: S
authors.lastname: Das
authors.affiliation: National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India.
authors.forename: Saurabh
authors.initials: S
authors.lastname: Badoni
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: 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: International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru 502324, Telangana, India.
authors.forename: C L L
authors.initials: CL
authors.lastname: Gowda
authors.affiliation: International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru 502324, Telangana, India.
authors.forename: Shivali
authors.initials: S
authors.lastname: Sharma
authors.affiliation: International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru 502324, Telangana, India.
authors.forename: Sube
authors.initials: S
authors.lastname: Singh
authors.affiliation: National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India.
authors.forename: Akhilesh K
authors.initials: AK
authors.lastname: Tyagi
authors.affiliation: National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India swarup@nipgr.ac.in swarupdbt@gmail.com.
authors.forename: Swarup K
authors.initials: SK
authors.lastname: Parida
mesh_terms: D000483:Alleles; D001483:Base Sequence; D029863:Cicer / Q000737:chemistry / Q000145:classification / Q000235:genetics*; D017124:Conserved Sequence; D005819:Genetic Markers; D018745:Genome, Plant; D023281:Genomics; D005838:Genotype; D018895:Microsatellite Repeats; D008969:Molecular Sequence Data; D010802:Phylogeny; D010940:Plant Proteins / Q000737:chemistry / Q000235:genetics; D040641:Quantitative Trait Loci; D012639:Seeds / Q000737:chemistry / Q000145:classification / Q000235:genetics; D016415:Sequence Alignment
chemical_list: D005819:Genetic Markers; D010940:Plant Proteins
keywords: CNMS; Chickpea; Cicer arietinum; SNPs; eQTLs; microsatellites; seed weight; transcription factor.