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Genome-wide development and deployment of informative intron-spanning and intron-length polymorphism markers for genomics-assisted breeding applications in chickpea

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Title Genome-wide development and deployment of informative intron-spanning and intron-length polymorphism markers for genomics-assisted breeding applications in chickpea
 
Creator Srivastava, Rishi
Bajaj, Deepak
Sayal, Yogesh K.
Meher, Prabina K.
Upadhyaya, Hari D.
Kumar, Rajendra
Tripathi, Shailesh
Bharadwaj, Chellapilla
Rao, Atmakuri R.
Parida, Swarup K.
 
Subject Genetic map
ILP
ISM
Marker
QTL
Chickpea
 
Description Accepted date: 24 August 2016
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: 0.65 cM) 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.
The authors gratefully acknowledge the financial support for this study provided by a research grant from the Department of Biotechnology (DBT), Government of India (102/IFD/SAN/2161/2013-14). We are thankful to the Editor and reviewers for critically evaluating the manuscript and providing constructive comments.
 
Date 2016-09-23T11:50:53Z
2016-09-23T11:50:53Z
2016
 
Type Article
 
Identifier Plant Science, 252: 374-387
0168-9452
http://59.163.192.83:8080/jspui/handle/123456789/685
http://www.sciencedirect.com/science/article/pii/S0168945216303715
http://dx.doi.org/10.1016/j.plantsci.2016.08.013
 
Language en_US
 
Publisher Elsevier B.V.