ArticleBMC plant biology2011
Analysis of BAC-end sequences (BESs) and development of BES-SSR markers for genetic mapping and hybrid purity assessment in pigeonpea (Cajanus spp.).
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 53 papers.
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Who cites it
53 citing papers in PubMed, 151 citations in OpenAlex.
- Genome-wide discovery, characterization, and validation of novel SSR markers in clove (Syzygium aromaticum) and their application in genetic analysis.BMC plant biology · 2026Article
- Marker-trait associations for ideotypic traits in pigeonpea (Cajanus cajan L.).Molecular biology reports · 2026Article
- Comprehensive genome-wide identification and transferability of chromosome-specific highly variable microsatellite markers from citrus species.Scientific reports · 2023Article
- BAC-FISH Based Physical Map of Endangered CatfishInternational journal of molecular sciences · 2022Article
- Genetic Augmentation of Legume Crops Using Genomic Resources and Genotyping Platforms for Nutritional Food Security.Plants (Basel, Switzerland) · 2022Review
- Comprehensive Characterization and Validation of Chromosome-Specific Highly Polymorphic SSR Markers From Pomegranate (Frontiers in plant science · 2021Article
- Cross-genera amplification ofPhysiology and molecular biology of plants : an international journal of functional plant biology · 2020Article
- Analysis of Genetic Diversity and Population Structure of Pigeonpea [Plants (Basel, Switzerland) · 2020Article
- Mapping QTL for important seed traits in an interspecific F2 population of pigeonpea.3 Biotech · 2020Article
- Genomics-assisted breeding for pigeonpea improvement.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2020Review
- Genome wide identification, characterization and validation of novel miRNA-based SSR markers in pomegranate (Physiology and molecular biology of plants : an international journal of functional plant biology · 2020Article
- Genotyping-by-sequencing and multilocation evaluation of two interspecific backcross populations identify QTLs for yield-related traits in pigeonpea.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2020Article
- Bambara groundnut: an exemplar underutilised legume for resilience under climate change.Planta · 2019Review
- A decade of Tropical Legumes projects: Development and adoption of improved varieties, creation of market-demand to benefit smallholder farmers and empowerment of national programmes in sub-Saharan Africa and South Asia.Plant breeding = Zeitschrift fur Pflanzenzuchtung · 2019Article
- Genomics, genetics and breeding of tropical legumes for better livelihoods of smallholder farmers.Plant breeding = Zeitschrift fur Pflanzenzuchtung · 2019Review
- 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
- Toward the sequence-based breeding in legumes in the post-genome sequencing era.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2019Review
- Adapting legume crops to climate change using genomic approaches.Plant, cell & environment · 2019Review
- Development and Application of High-Density AxiomThe plant genome · 2018Article
- Molecular mapping and inheritance of restoration of fertility (Rf) in A4 hybrid system in pigeonpea (Cajanus cajan (L.) Millsp.).TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2018Article
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Authors and funding
19 authors at 10 institutions in 4 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundPigeonpea [Cajanus cajan (L.) Millsp.] is an important legume crop of rainfed agriculture. Despite of concerted research efforts directed to pigeonpea improvement, stagnated productivity of pigeonpea during last several decades may be accounted to prevalence of various biotic and abiotic constraints and the situation is exacerbated by availability of inadequate genomic resources to undertake any molecular breeding programme for accelerated crop improvement. With the objective of enhancing genomic resources for pigeonpea, this study reports for the first time, large scale development of SSR markers from BAC-end sequences and their subsequent use for genetic mapping and hybridity testing in pigeonpea.
resultsA set of 88,860 BAC (bacterial artificial chromosome)-end sequences (BESs) were generated after constructing two BAC libraries by using HindIII (34,560 clones) and BamHI (34,560 clones) restriction enzymes. Clustering based on sequence identity of BESs yielded a set of >52K non-redundant sequences, comprising 35 Mbp or >4% of the pigeonpea genome. These sequences were analyzed to develop annotation lists and subdivide the BESs into genome fractions (e.g., genes, retroelements, transpons and non-annotated sequences). Parallel analysis of BESs for microsatellites or simple sequence repeats (SSRs) identified 18,149 SSRs, from which a set of 6,212 SSRs were selected for further analysis. A total of 3,072 novel SSR primer pairs were synthesized and tested for length polymorphism on a set of 22 parental genotypes of 13 mapping populations segregating for traits of interest. In total, we identified 842 polymorphic SSR markers that will have utility in pigeonpea improvement. Based on these markers, the first SSR-based genetic map comprising of 239 loci was developed for this previously uncharacterized genome. Utility of developed SSR markers was also demonstrated by identifying a set of 42 markers each for two hybrids (ICPH 2671 and ICPH 2438) for genetic purity assessment in commercial hybrid breeding programme.
conclusionIn summary, while BAC libraries and BESs should be useful for genomics studies, BES-SSR markers, and the genetic map should be very useful for linking the genetic map with a future physical map as well as for molecular breeding in pigeonpea.
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