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Title: Comprehensive transcriptome assembly of chickpea (Cicer arietinum L.) using Sanger and next generation sequencing platforms: development and applications

Author
item KUDAPA, HIMABINDU - International Crops Research Institute For Semi-Arid Tropics (ICRISAT) - India
item AZAM, SARWAR - International Crops Research Institute For Semi-Arid Tropics (ICRISAT) - India
item SHARPE, ANDREW - National Research Council - Canada
item TARAN, BUNYAMIN - University Of Saskatchewan
item LI, RONG - National Research Council - Canada
item DEONOVIC, BENJAMIN - University Of Iowa
item CAMERON, CONNOR - National Center For Genome Resources
item FARMER, ANDREW - National Center For Genome Resources
item Cannon, Steven
item VARSHNEY, RAJEEV - International Crops Research Institute For Semi-Arid Tropics (ICRISAT) - India

Submitted to: PLOS ONE
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 12/3/2013
Publication Date: 1/23/2014
Citation: Kudapa, H., Azam, S., Sharpe, A.G., Taran, B., Li, R., Deonovic, B., Cameron, C., Farmer, A.D., Cannon, S.B., Varshney, R.K. 2014. Comprehensive transcriptome assembly of chickpea (Cicer arietinum L.) using Sanger and next generation sequencing platforms: development and applications. PLoS One. 9(1):e86039. DOI: 10.1371/journal.pone.0086039.

Interpretive Summary: Chickpea is one of the world's important crop plants as it is able to enrich the soil with nitrogen and is used in many diverse climates and cropping systems. Chickpea is high in protein and other nutrients and is a versatile core ingredient in many cuisines. There is a strong need for development of improved varieties -- for higher yield, increased tolerance to stresses such as drought and heat and cold, and better resistance to diseases and pests. Such breeding efforts depend on strong genetic information resources such as gene sequences and genetic markers. This paper describes a report of the nearly complete set of gene sequences, called a "transcriptome assembly;" and a large set of genetic markers derived from these sequences. The genetic markers can be used by plant breeders as convenient guides for selecting plants with desired characteristics. The gene sequences and new markers can be used for a variety of applications such as gene discovery, marker-trait association, and diversity analysis, in order to advance genetics research and breeding applications in chickpea.

Technical Abstract: A high-quality transcriptome assembly for chickpea has been developed using ~135 million Illumina single-end reads, 7.12 million single-end FLX/454 reads, and 139 thousand Sanger expressed sequence tags (ESTs). This hybrid transcriptome assembly, which we refer to as the "Cicer arietinum Transcriptome Assembly version 2" or "CaTA v2," is available at http://data.comparative-legumes.org/transcriptomes/cicar/lista_cicar-201201. The CaTA v2 comprises 46,369 transcript assembly contigs (TACs), and has an N50 length of 1,726 bp and has a maximum contig size of 15,644 bp. We used the CaTA v2 to develop a large number of candidate markers around SSRs and intron sequences. We identified 5,342 simple sequence repeats (SSRs), and used these to design primers for 2,474 markers. We also compared the CaTA v2 to the Medicago genome in order to predict 14,153 candidate intron spanning region (ISR) markers. These have the advantage that the likely relative locations of the ISR markers can be inferred from their locations in Medicago, as Medicago and Cicer are syntenic over most of their chromosomes. To test and validate the ISRs for marker conversion rate and placement accuracy, a set of 158 ISRs were used to test the putative chromosomal placements. Of these 158, 56 markers (35%) gave scorable amplicons (using PCR in five genotypes). In these 56 ISR markers (from all eight chickpea linkage groups), 20% (11 markers) were polymorphic, with an average polymorphic information content (PIC) of 0.27. The hybrid transcriptome assembly and new markers can be used for a variety of applications such as gene discovery, marker-trait association, and diversity analysis, to advance genetics research and breeding applications in chickpea; and will serve as a useful resource to enhance chickpea genetic research and molecular breeding.