ArticleMolecular plant2012
A comprehensive transcriptome assembly of Pigeonpea (Cajanus cajan L.) using sanger and second-generation sequencing platforms.
Article in Molecular plant, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 37 papers.
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Who cites it
37 citing papers in PubMed.
- Marker-trait associations for ideotypic traits in pigeonpea (Cajanus cajan L.).Molecular biology reports · 2026Article
- Systems biology for crop improvement.The plant genome · 2021Review
- Comparative Time Series RNA-seq Analysis of Pigeonpea Root Tissues in Response toFrontiers in fungal biology · 2021Article
- Genomics-assisted breeding for pigeonpea improvement.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2020Review
- Genetic Divergence and Relationship AmongFrontiers in genetics · 2020Article
- An "Axiom Cajanus SNP Array" based high density genetic map and QTL mapping for high-selfing flower and seed quality traits in pigeonpea.BMC genomics · 2019Article
- De novo assembly of transcriptomes, mining, and development of novel EST-SSR markers in Curcuma alismatifolia (Zingiberaceae family) through Illumina sequencing.Scientific reports · 2019Article
- Comprehensive Stress-Based De Novo Transcriptome Assembly and Annotation of Guar (International journal of genomics · 2019Article
- Development and application of genomic resources for comparative and translational genomics in legumes through leveraging genomic sequence ofJournal of genetics · 2018Article
- Association mapping to discover significant marker-trait associations for resistance against fusarium wilt variant 2 in pigeonpea [Cajanus cajan (L.) Millspaugh] using SSR markers.Journal of applied genetics · 2017Article
- De novo transcriptomic analysis of cowpea (Vigna unguiculata L. Walp.) for genic SSR marker development.BMC genetics · 2017Article
- New Hypervariable SSR Markers for Diversity Analysis, Hybrid Purity Testing and Trait Mapping in Pigeonpea [Frontiers in plant science · 2017Article
- Generation and Characterisation of a Reference Transcriptome for Lentil (Lens culinaris Medik.).International journal of molecular sciences · 2016Article
- First-generation HapMap in Cajanus spp. reveals untapped variations in parental lines of mapping populations.Plant biotechnology journal · 2016Article
- Genome-wide dissection of AP2/ERF and HSP90 gene families in five legumes and expression profiles in chickpea and pigeonpea.Plant biotechnology journal · 2016Article
- Article
- Comparative analysis of genome-wide Mlo gene family in Cajanus cajan and Phaseolus vulgaris.Genetica · 2016Article
- Comparative transcriptome analysis of Gastrodia elata (Orchidaceae) in response to fungus symbiosis to identify gastrodin biosynthesis-related genes.BMC genomics · 2016Article
- Emerging Genomic Tools for Legume Breeding: Current Status and Future Prospects.Frontiers in plant science · 2016Review
- Genomics-assisted breeding for boosting crop improvement in pigeonpea (Cajanus cajan).Frontiers in plant science · 2015Review
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19 authors.
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Abstract
A comprehensive transcriptome assembly for pigeonpea has been developed by analyzing 128.9 million short Illumina GA IIx single end reads, 2.19 million single end FLX/454 reads, and 18 353 Sanger expressed sequenced tags from more than 16 genotypes. The resultant transcriptome assembly, referred to as CcTA v2, comprised 21 434 transcript assembly contigs (TACs) with an N50 of 1510 bp, the largest one being ~8 kb. Of the 21 434 TACs, 16 622 (77.5%) could be mapped on to the soybean genome build 1.0.9 under fairly stringent alignment parameters. Based on knowledge of intron junctions, 10 009 primer pairs were designed from 5033 TACs for amplifying intron spanning regions (ISRs). By using in silico mapping of BAC-end-derived SSR loci of pigeonpea on the soybean genome as a reference, putative mapping positions at the chromosome level were predicted for 6284 ISR markers, covering all 11 pigeonpea chromosomes. A subset of 128 ISR markers were analyzed on a set of eight genotypes. While 116 markers were validated, 70 markers showed one to three alleles, with an average of 0.16 polymorphism information content (PIC) value. In summary, the CcTA v2 transcript assembly and ISR markers will serve as a useful resource to accelerate genetic research and breeding applications in pigeonpea.
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