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.
Highlights
IntroductionCultivated peanut, or groundnut (Arachis hypogaea L.), is a major economic crop in most tropical and subtropical areas of the world and represents a significant source of oil and protein for human nutrition
Cultivated peanut, or groundnut (Arachis hypogaea L.), is an important oilseed crop with an allotetraploid genome (AABB, 2n = 4x = 40)
To enable multiplex sequencing of the libraries, we used a set of molecular identifying sequences (MIDs) ranging in length from 5 bp to 8 bp that allowed reads to be assigned to unique individuals
Summary
Cultivated peanut, or groundnut (Arachis hypogaea L.), is a major economic crop in most tropical and subtropical areas of the world and represents a significant source of oil and protein for human nutrition. Because this species is a self-pollinating allotetraploid (AABB, 2n = 4× = 40) with a large genome size (2800 Mb/1C) and a narrow genetic base, leading to very low DNA polymorphism, the development of molecular markers and genomic resources in peanut has always been a formidable task [1,2,3]. Until recently, only sporadic SNP markers had been developed in cultivated peanuts, and no SNP marker-based genetic map has been previously reported
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