A genome-scale integrated approach aids in genetic dissection of complex flowering time trait in chickpea
Impact factor: 2.304 (Year: 2015)
MetadataShow full item record
Hari D. Upadhyaya, Swarup K. Parida, Deepak Bajaj, S. K. Das, C. L. L. Gowda, Vinay Kumar, Mohan C. Saxena, Shivali Sharma, Shailesh Tripathi, Akhilesh K. Tyagi. (28/9/2015). A genome-scale integrated approach aids in genetic dissection of complex flowering time trait in chickpea. Plant Molecular Biology, 1, pp. 1-18.
A combinatorial approach of candidate gene-based association analysis and genome-wide association study (GWAS) integrated with QTL mapping, differential gene expression profiling and molecular haplotyping was deployed in the present study for quantitative dissection of complex flowering time trait in chickpea. Candidate gene-based association mapping in a flowering time association panel (92 diverse desi and kabuli accessions) was performed by employing the genotyping information of 5724 SNPs discovered from 82 known flowering chickpea gene orthologs of Arabidopsis and legumes as well as 832 gene-encoding transcripts that are differentially expressed during flower development in chickpea. GWAS using both genome-wide GBS- and candidate gene-based genotyping data of 30,129 SNPs in a structured population of 92 sequenced accessions (with 200–250 kb LD decay) detected eight maximum effect genomic SNP loci (genes) associated (34 % combined PVE) with flowering time. Six flowering time-associated major genomic loci harbouring five robust QTLs mapped on a high-resolution intra-specific genetic linkage map were validated (11.6–27.3 % PVE at 5.4–11.7 LOD) further by traditional QTL mapping. The flower-specific expression, including differential up- and down-regulation (>three folds) of eight flowering time-associated genes (including six genes validated by QTL mapping) especially in early flowering than late flowering contrasting chickpea accessions/mapping individuals during flower development was evident. The gene haplotype-based LD mapping discovered diverse novel natural allelic variants and haplotypes in eight genes with high trait association potential (41 % combined PVE) for flowering time differentiation in cultivated and wild chickpea. Taken together, eight potential known/candidate flowering time-regulating genes [efl1 (early flowering 1), FLD (Flowering locus D), GI (GIGANTEA), Myb (Myeloblastosis), SFH3 (SEC14-like 3), bZIP (basic-leucine zipper), bHLH (basic helix-loop-helix) and SBP (SQUAMOSA promoter binding protein)], including novel markers, QTLs, alleles and haplotypes delineated by aforesaid genome-wide integrated approach have potential for marker-assisted genetic improvement and unravelling the domestication pattern of flowering time in chickpea.
- Agricultural Research Knowledge 
plant breeding; gbs; snp; gwas; Chickpea
Showing items related by title, author, creator and subject.
Title: Adapting Agriculture to Climate Change: A Synopsis of Coordinated National Crop Wild Relative Seed Collecting Programs across Five Continents Author(s)Eastwood, Ruth; Tambam, Beri B.; Aboagye, Lawrence M; Akparov, Zeynal; Aladele, Sunday E.; Allen, Richard G.; Amri, Ahmed; Anglin, Noelle; Araya, Rodolfo; Espinoza, Griselda Arrieta; Asgerov, Aydin; Awang, Khadijah; Awas, Tesfaye; Barata, Ana Maria; Boateng, Samuel Kwasi; Brehm, Joana Magos; Braidy, Joelle; Breman, Elinor; Angulo, Arturo Brenes; Burle, Marília L.; Álvarez, Nora P. Castañeda; Casimiro, Pedro; Chaves, Nestor; Clemente, Adelaide S; Cockel, Christopher; Davey, Alexandra; De la Rosa, Lucía; Debouck, Daniel; Dempewolf, Hannes; Dokmak, Hiba; Ellis, David; Faruk, Aisyah; Freitas, Cátia; Galstyan, Sona; García, Rosa M; Ghimire, Krishna H; Guarino, Luigi; Harker, Ruth; Hope, Roberta; Humphries, Alan W; Jamora, Nelissa; Jatoi, Shakeel Ahmad; Khutsishvili, Manana; Kikodze, David; Kyratzis, Angelos C.; Lobos, Pedro León; Liu, Udayangani; Mainali, Ram P; Mammadov, Afig T.; Manrique, Norma; Manzella, Daniele; Ali, Mohd Shukri Mat; Medeiros, Marcelo B; Guzman, María A. Mérida; Pantsulaia, Tsira Mikatadze; Mohamed, El Tahir Ibrahim; Altamirano, Álvaro Monteros; Morales, Aura; Muller, Jonas V; Mulumba, John; Nersesyan, Anush; Nobrega, Humberto; Nyamongo, Desterio; Obreza, Matija; Okere, Anthony U; Orsenigo, Simone; Klose, Fernando Ortega; Papikyan, Astghik; Pearce, Timothy R; Pinheiro de Carvalho, Miguel A. A.; Prohens, Jaime; Rossi, Graziano; Salas, Alberto; Singh, Deepak; Siddiqui, Sadar Uddin; Smith, Paul P; Sotomayor, Diego A; Tacán, Marcelo; Tapia, César; Toledo, Álvaro; Toll, Jane; Vu, Dang Toan; Dang Vu, Tuong; Way, Michael J; Yazbek, Mariana; Zorrilla, Cinthya; Kilian, BenjaminDate: 2022-07-13Type: Journal ArticleStatus: Open accessThe Adapting Agriculture to Climate Change Project set out to improve the diversity, quantity, and accessibility of germplasm collections of crop wild relatives (CWR). Between 2013 and 2018, partners in 25 countries, heirs ...
Title: Peer-Reviewed Literature on Grain Legume Species in the WoS (1980–2018): A Comparative Analysis of Soybean and Pulses Author(s)Magrini, Marie-Benoit; Cabanac, Guillaume; Lascialfari, Matteo; Plumecocq, Gaël; Amiot, Marie Josephe; Anton, Marc; Arvisenet, Gaëlle; Baranger, Alain; Bedoussac, Laurent; Chardigny, Jean-Michel; Duc, Gérard; Jeuffroy, Marie-Hélène; Journet, Etienne-Pascal; Juin, Hervé; Larre, Colette; Leiser, Hugues; Micard, Valérie; Millot, Dominique; Pilet-Nayel, Marie-Laure; Nguyen-Thé, Christophe; Salord, Tristan; Voisin, Anne-Sophie; Walrand, Stephane; Wery, JacquesDate: 2019-12-02Type: Journal ArticleStatus: Open accessGrain-legume crops are important for ensuring the sustainability of agrofood systems. Among them, pulse production is subject to strong lock-in compared to soya, the leading worldwide crop. To unlock the situation and ...
Title: Minutes of high-level guidance not captured by the "pink Aide Memoire" Author(s)Bassi, Filippo; Sanchez-Garcia, Miguel; Baum, MichaelDate: 2022-12-30Type: ReportStatus: Timeless limited accessCWANA Genetic Innovation and Regional CGIAR Initiatives consultation meeting with NARES to develop guiding principles up to 2030 for the development of genetic innovations targeted to the region, meeting in Turkiye, 13-15 ...