ArticleBMC genomics2014
Construction of a SNP-based genetic linkage map in cultivated peanut based on large scale marker development using next-generation double-digest restriction-site-associated DNA sequencing (ddRADseq).
Article in BMC genomics, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 78 papers.
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Who cites it
78 citing papers in PubMed, 141 citations in OpenAlex.
- Surprisingly frequent chromosomal instability in cultivated peanut.The Plant journal : for cell and molecular biology · 2025Article
- High-density genetic map construction using whole-genome resequencing of theFrontiers in plant science · 2025Article
- High-Density Genetic Map Construction and Quantitative Trait Locus Analysis of Fruit- and Oil-Related Traits inInternational journal of molecular sciences · 2024Article
- Detection of two homologous major QTLs and development of diagnostic molecular markers for sucrose content in peanut.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2024Article
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- Genome-wide association study as a powerful tool for dissecting competitive traits in legumes.Frontiers in plant science · 2023Review
- CAPG: comprehensive allopolyploid genotyper.Bioinformatics (Oxford, England) · 2023Article
- Multiple Variant Calling Pipelines in Wheat Whole Exome Sequencing.International journal of molecular sciences · 2021Article
- Construction of ddRADseq-Based High-Density Genetic Map and Identification of Quantitative Trait Loci for Trans-resveratrol Content in Peanut Seeds.Frontiers in plant science · 2021Article
- Identification of Sex-Specific Markers Through 2b-RAD Sequencing in the Sea Urchin (Frontiers in genetics · 2021Article
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- Pod and Seed Trait QTL Identification To Assist Breeding for Peanut Market Preferences.G3 (Bethesda, Md.) · 2020Article
- Translational genomics for achieving higher genetic gains in groundnut.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2020Review
- Discovery of two novel and adjacent QTLs on chromosome B02 controlling resistance against bacterial wilt in peanut variety Zhonghua 6.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2020Article
- Mapping quantitative trait loci (QTLs) and estimating the epistasis controlling stem rot resistance in cultivated peanut (Arachis hypogaea).TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2020Article
- Article
- Comparison of SNP Calling Pipelines and NGS Platforms to Predict the Genomic Regions Harboring Candidate Genes for Nodulation in Cultivated Peanut.Frontiers in genetics · 2020Article
- A new source of root-knot nematode resistance from Arachis stenosperma incorporated into allotetraploid peanut (Arachis hypogaea).Scientific reports · 2019Article
- Genetics, genomics and breeding of groundnut (Plant breeding = Zeitschrift fur Pflanzenzuchtung · 2019Review
18 more citing papers are in PubMed but not listed here.
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Authors and funding
10 authors at 4 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundCultivated peanut, or groundnut (Arachis hypogaea L.), is an important oilseed crop with an allotetraploid genome (AABB, 2n=4x=40). In recent years, many efforts have been made to construct linkage maps in cultivated peanut, but almost all of these maps were constructed using low-throughput molecular markers, and most show a low density, directly influencing the value of their applications. With advances in next-generation sequencing (NGS) technology, the construction of high-density genetic maps has become more achievable in a cost-effective and rapid manner. The objective of this study was to establish a high-density single nucleotide polymorphism (SNP)-based genetic map for cultivated peanut by analyzing next-generation double-digest restriction-site-associated DNA sequencing (ddRADseq) reads.
resultsWe constructed reduced representation libraries (RRLs) for two A. hypogaea lines and 166 of their recombinant inbred line (RIL) progenies using the ddRADseq technique. Approximately 175 gigabases of data containing 952,679,665 paired-end reads were obtained following Solexa sequencing. Mining this dataset, 53,257 SNPs were detected between the parents, of which 14,663 SNPs were also detected in the population, and 1,765 of the obtained polymorphic markers met the requirements for use in the construction of a genetic map. Among 50 randomly selected in silico SNPs, 47 were able to be successfully validated. One linkage map was constructed, which was comprised of 1,685 marker loci, including 1,621 SNPs and 64 simple sequence repeat (SSR) markers. The map displayed a distribution of the markers into 20 linkage groups (LGs A01-A10 and B01-B10), spanning a distance of 1,446.7 cM. The alignment of the LGs from this map was shown in comparison with a previously integrated consensus map from peanut.
conclusionsThis study showed that the ddRAD library combined with NGS allowed the rapid discovery of a large number of SNPs in the cultivated peanut. The first high density SNP-based linkage map for A. hypogaea was generated that can serve as a reference map for cultivated Arachis species and will be useful in genetic mapping. Our results contribute to the available molecular marker resources and to the assembly of a reference genome sequence for the peanut.
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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.