title: A high-density genetic map for soybean based on specific length amplified fragment sequencing.
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.
authors.affiliation: College of Agriculture, Northeast Agricultural University, Harbin, Heilongjiang, People's Republic of China.
authors.forename: Zhaoming
authors.initials: Z
authors.lastname: Qi
authors.affiliation: Biomarker Technologies Corporation, Beijing, China.
authors.forename: Long
authors.initials: L
authors.lastname: Huang
authors.affiliation: College of Agriculture, Northeast Agricultural University, Harbin, Heilongjiang, People's Republic of China.
authors.forename: Rongsheng
authors.initials: R
authors.lastname: Zhu
authors.affiliation: College of Agriculture, Northeast Agricultural University, Harbin, Heilongjiang, People's Republic of China.
authors.forename: Dawei
authors.initials: D
authors.lastname: Xin
authors.affiliation: The Crop Research and Breeding Center of Land-Reclamation of Heilongjiang Province, Harbin, Heilongjiang, People's Republic of China.
authors.forename: Chunyan
authors.initials: C
authors.lastname: Liu
authors.affiliation: The Crop Research and Breeding Center of Land-Reclamation of Heilongjiang Province, Harbin, Heilongjiang, People's Republic of China.
authors.forename: Xue
authors.initials: X
authors.lastname: Han
authors.affiliation: The Crop Research and Breeding Center of Land-Reclamation of Heilongjiang Province, Harbin, Heilongjiang, People's Republic of China.
authors.forename: Hongwei
authors.initials: H
authors.lastname: Jiang
authors.affiliation: Biomarker Technologies Corporation, Beijing, China.
authors.forename: Weiguo
authors.initials: W
authors.lastname: Hong
authors.affiliation: The Crop Research and Breeding Center of Land-Reclamation of Heilongjiang Province, Harbin, Heilongjiang, People's Republic of China.
authors.forename: Guohua
authors.initials: G
authors.lastname: Hu
authors.affiliation: Biomarker Technologies Corporation, Beijing, China.
authors.forename: Hongkun
authors.initials: H
authors.lastname: Zheng
authors.affiliation: College of Agriculture, Northeast Agricultural University, Harbin, Heilongjiang, People's Republic of China.
authors.forename: Qingshan
authors.initials: Q
authors.lastname: Chen
mesh_terms: D054458:Amplified Fragment Length Polymorphism Analysis; D002874:Chromosome Mapping; D032461:Chromosomes, Plant / Q000235:genetics; D018744:DNA, Plant / Q000235:genetics; D005819:Genetic Markers; D018745:Genome, Plant; D006239:Haplotypes; D059014:High-Throughput Nucleotide Sequencing; D006824:Hybridization, Genetic; D020641:Polymorphism, Single Nucleotide; D040641:Quantitative Trait Loci; D017422:Sequence Analysis, DNA; D013025:Glycine max / Q000235:genetics*
chemical_list: D018744:DNA, Plant; D005819:Genetic Markers