title: 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).
abstract: BACKGROUND
  Cultivated 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.
  
  
  RESULTS
  We 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.
  
  
  CONCLUSIONS
  This 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.
authors.forename: Xiaojing
authors.initials: X
authors.lastname: Zhou
authors.forename: Youlin
authors.initials: Y
authors.lastname: Xia
authors.forename: Xiaoping
authors.initials: X
authors.lastname: Ren
authors.forename: Yulin
authors.initials: Y
authors.lastname: Chen
authors.forename: Li
authors.initials: L
authors.lastname: Huang
authors.forename: Shunmou
authors.initials: S
authors.lastname: Huang
authors.forename: Boshou
authors.initials: B
authors.lastname: Liao
authors.forename: Yong
authors.initials: Y
authors.lastname: Lei
authors.forename: Liyin
authors.initials: L
authors.lastname: Yan
authors.affiliation: Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan 430062, Hubei, People's Republic of China. peanutlab@oilcrops.cn.
authors.forename: Huifang
authors.initials: H
authors.lastname: Jiang
mesh_terms: D010367:Arachis / Q000235:genetics*; D002874:Chromosome Mapping; D019295:Computational Biology; D015723:Gene Library; D008040:Genetic Linkage; D018745:Genome, Plant; D005838:Genotype; D059014:High-Throughput Nucleotide Sequencing; D018895:Microsatellite Repeats; D020641:Polymorphism, Single Nucleotide; D040641:Quantitative Trait Loci; D017422:Sequence Analysis, DNA; D057891:Tetraploidy