A high-density genetic map for soybean based on specific length amplified fragment sequencing.

Zhaoming Qi,Xue Han,Hongwei Jiang,Hongkun Zheng,Weiguo Hong,Rongsheng Zhu,Chunyan Liu,Long Huang,Qingshan Chen,Guohua Hu,Dawei Xin,Jin-Song Zhang

doi:10.1371/journal.pone.0104871

Abstract

Soybean is an important oil seed crop, but very few high-density genetic maps have been published for this species. Specific length amplified fragment sequencing (SLAF-seq) is a recently developed high-resolution strategy for large scale de novo discovery and genotyping of single nucleotide polymorphisms. SLAF-seq was employed in this study to obtain sufficient markers to construct a high-density genetic map for soybean. In total, 33.10 Gb of data containing 171,001,333 paired-end reads were obtained after preprocessing. The average sequencing depth was 42.29 in the Dongnong594, 56.63 in the Charleston, and 3.92 in each progeny. In total, 164,197 high-quality SLAFs were detected, of which 12,577 SLAFs were polymorphic, and 5,308 of the polymorphic markers met the requirements for use in constructing a genetic map. The final map included 5,308 markers on 20 linkage groups and was 2,655.68 cM in length, with an average distance of 0.5 cM between adjacent markers. To our knowledge, this map has the shortest average distance of adjacent markers for soybean. We report here a high-density genetic map for soybean. The map was constructed using a recombinant inbred line population and the SLAF-seq approach, which allowed the efficient development of a large number of polymorphic markers in a short time. Results of this study will not only provide a platform for gene/quantitative trait loci fine mapping, but will also serve as a reference for molecular breeding of soybean.

Highlights

Soybean, Glycine max (L.) Merr., is a major protein source and represents the world’s leading oilseed crop, accounting for approximately 56% of global oilseed production [1]
Feasibility and advantages of specific length amplified fragment (SLAF) sequencing for developing markers
Differences between RAD-seq,SLAF is measured by sequencing the paired-ends of the sequence-specific restriction fragment length, RAD sequence is a sequence of measured randomly interrupted after the restriction sites surrounding

Summary

Introduction

Glycine max (L.) Merr., is a major protein source and represents the world’s leading oilseed crop, accounting for approximately 56% of global oilseed production [1]. Because of its economic importance and nutritional value, the study of soybean genetics and molecular biology has progressed rapidly in the past 20 years. Keim et al [2] constructed a soybean genetic map using restriction fragment length polymorphism (RFLP) markers, and Shoemaker et al [3] and Lark et al [4] simultaneously published molecular linkage maps. Choi et al [7] constructed a soybean transcript map and analyzed the gene distribution, haplotypes, and single nucleotide polymorphisms (SNPs). With recent advances in genome sequencing, Hyten et al [8,9] built two high density integrated genetic linkage maps of soybean based genome sequencing and high-throughput SNP genotyping

Methods

Results

Conclusion