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

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.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-15-351) contains supplementary material, which is available to authorized users.

Double‐digest RADseq loci using standard Illumina indexes improve deep and shallow phylogenetic resolution of Lophodermium, a widespread fungal endophyte of pine needles

“…The double‐digest RADseq (ddRADseq; Peterson, Weber, Kay, Fisher, & Hoekstra, 2012), a variation of the original method (Baird et al., 2008), improves on depth of coverage per locus by optimizing sequencing effort and reducing missing genotypes. The protocol is flexible, allowing for easy optimization for different organisms, genome sizes, genetic diversity, and scientific questions (Mastretta‐Yanes et al., 2015; Nieto‐Montes de Oca et al., 2017; Recknagel, Elmer, & Meyer, 2013; Zhou et al., 2014). Consequently, numerous modifications or improvements of ddRADseq are being continually proposed (Franchini, Parera, Kautt, & Meyer, 2017; Heffelfinger et al., 2014; Recknagel, Jacobs, Herzyk, & Elmer, 2015).…”

The genome sequences of Arachis duranensis and Arachis ipaensis, the diploid ancestors of cultivated peanut

“…Higher percentages indicate less Figure 7 Identification of genetic exchange between subgenomes in cultivated peanut. The top graph depicts the result of recombination between A04 and B04 in RIL028, and, for comparison, the bottom graph shows RIL025, a typical line where this type of recombination has not occurred (lines described in Zhou et al 41 ). The y axis shows log 2 -transformed ratios of densities of mapping for restriction site-associated sequence reads along the diploid chromosomal pseudomolecules divided by the mapping densities of a parental line.…”

“…We used the chromosomal pseudomolecules to investigate the frequency of recombination between A and B subgenomes in 166 cultivated peanut RILs described in a previous study 41 . To do this, we calculated the mapping densities of restriction site-associated sequence reads from these RILs and their parental lines along the chromosomal pseudomolecules.…”

“…Of the marker sequences from three maps 21,41 , 83%, 83% and 94% were assigned by sequence similarity searches to the expected diploid chromosomal pseudomolecules (Supplementary Data Set 6). When visualized as plots along the chromosomal pseudomolecules, the diploid A-genome chromosomes were distinctly less similar to A. hypogaea sequences than the B-genome chromosomes (Fig.…”

“…Considering the date of divergence of the A and B genomes as 2.16 million years ago (from K S values), this gives an Arachis genome-wide mutation rate of 1.6 × 10 −8 mutations per base per year (within the range of 1-2 × 10 −8 calculated for other plants 44 ). This mutation rate and the divergence of the most conserved chromosomes (presumably the ones that have undergone the least recombination between subgenomes; A01 and B07) gives an estimate of the divergence time of A. duranensis V14167 from the A subgenome of A. hypogaea as ~247,000 years and for the divergence time of A. ipaensis from the B subgenome of A. hypogaea as a remarkably recent ~9,400 years.We used the chromosomal pseudomolecules to investigate the frequency of recombination between A and B subgenomes in 166 cultivated peanut RILs described in a previous study 41 . To do this, we calculated the mapping densities of restriction site-associated sequence reads from these RILs and their parental lines along the chromosomal pseudomolecules.…”