ArticleBMC plant biology2011
Development of genic-SSR markers by deep transcriptome sequencing in pigeonpea [Cajanus cajan (L.) Millspaugh].
Article in BMC plant biology, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 109 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
109 citing papers in PubMed.
- De Novo Transcriptome Assembly of Rice Bean (Plants (Basel, Switzerland) · 2024Article
- The MYB Transcription FactorInternational journal of molecular sciences · 2024Article
- De novo transcriptome assembly of Dalbergia sissoo Roxb. (Fabaceae) under Botryodiplodia theobromae-induced dieback disease.Scientific reports · 2023Article
- De Novo Transcriptome Profiling for the Generation and Validation of Microsatellite Markers, Transcription Factors, and Database Development forInternational journal of molecular sciences · 2023Article
- Small cardamom genome: development and utilization of microsatellite markers from a draft genome sequence ofFrontiers in plant science · 2023Article
- Development of simple sequence repeat markers for sugarcane from data mining of expressed sequence tags.Frontiers in plant science · 2023Article
- Single trait versus principal component based association analysis for flowering related traits in pigeonpea.Scientific reports · 2022Article
- Genetic analysis of sucrose concentration in soybean seeds using a historical soybean genomic panel.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2022Article
- Occurrence of simple sequence repeats in cDNA sequences of safflower (Frontiers in plant science · 2022Article
- Article
- RNA-Seq Analysis of Developing Grains of Wheat to Intrigue Into the Complex Molecular Mechanism of the Heat Stress Response.Frontiers in plant science · 2022Article
- Genetic Diversity Study on Geographical Populations of the Multipurpose SpeciesFrontiers in plant science · 2022Article
- Article
- Development, characterization, functional annotation and validation of genomic and genic-SSR markers using de novo next generation sequencing in3 Biotech · 2021Article
- Full-length SMRT transcriptome sequencing and microsatellite characterization in Paulownia catalpifolia.Scientific reports · 2021Article
- Discovery of SNPs in important legumes through comparative genome analysis and conversion of SNPs into PCR-based markers.Journal of genetics · 2021Article
- Developments and Prospects in Imperative Underexploited Vegetable Legumes Breeding: A Review.International journal of molecular sciences · 2020Review
- Development of EST-SSR markers forPhysiology and molecular biology of plants : an international journal of functional plant biology · 2020Article
- Genomics-assisted breeding for pigeonpea improvement.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2020Review
- Characteristics of Microsatellites Mined from Transcriptome Data and the Development of Novel Markers inGenes · 2020Article
49 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
18 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundPigeonpea [Cajanus cajan (L.) Millspaugh], one of the most important food legumes of semi-arid tropical and subtropical regions, has limited genomic resources, particularly expressed sequence based (genic) markers. We report a comprehensive set of validated genic simple sequence repeat (SSR) markers using deep transcriptome sequencing, and its application in genetic diversity analysis and mapping.
resultsIn this study, 43,324 transcriptome shotgun assembly unigene contigs were assembled from 1.696 million 454 GS-FLX sequence reads of separate pooled cDNA libraries prepared from leaf, root, stem and immature seed of two pigeonpea varieties, Asha and UPAS 120. A total of 3,771 genic-SSR loci, excluding homopolymeric and compound repeats, were identified; of which 2,877 PCR primer pairs were designed for marker development. Dinucleotide was the most common repeat motif with a frequency of 60.41%, followed by tri- (34.52%), hexa- (2.62%), tetra- (1.67%) and pentanucleotide (0.76%) repeat motifs. Primers were synthesized and tested for 772 of these loci with repeat lengths of ≥ 18 bp. Of these, 550 markers were validated for consistent amplification in eight diverse pigeonpea varieties; 71 were found to be polymorphic on agarose gel electrophoresis. Genetic diversity analysis was done on 22 pigeonpea varieties and eight wild species using 20 highly polymorphic genic-SSR markers. The number of alleles at these loci ranged from 4-10 and the polymorphism information content values ranged from 0.46 to 0.72. Neighbor-joining dendrogram showed distinct separation of the different groups of pigeonpea cultivars and wild species. Deep transcriptome sequencing of the two parental lines helped in silico identification of polymorphic genic-SSR loci to facilitate the rapid development of an intra-species reference genetic map, a subset of which was validated for expected allelic segregation in the reference mapping population.
conclusionWe developed 550 validated genic-SSR markers in pigeonpea using deep transcriptome sequencing. From these, 20 highly polymorphic markers were used to evaluate the genetic relationship among species of the genus Cajanus. A comprehensive set of genic-SSR markers was developed as an important genomic resource for diversity analysis and genetic mapping in pigeonpea.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.