title: Construction of a high-density genetic map using specific-locus amplified fragments in sorghum.
abstract: Sorghum is mainly used as a human food and beverage source, playing an important role in the production of ethanol and other bio-industrial products. Thus it is regarded as a model crop for energy plants. Genetic map construction is the foundation for marker-assisted selection and gene cloning. So far several sorghum linkage maps have been reported using different kinds of molecular markers. However marker numbers and chromosome coverage are limited. As a result, it is difficult to get consistent results and the maps are hard to unify. In the present study, the genomes of 130 individuals consisting an F2population together with their parents were surveyed using a high-throughput sequencing technique. A high-density linkage map was constructed using specific-locus amplified fragments (SLAF) markers. This map can provide information and serve as a reference for effective gene exploration, and for marker assisted-breeding program.
  
  
  
  A high-throughput sequencing method was adopted to screen SLAF markers with 130 F2individuals from a cross between a grain sorghum variety, J204, and a sweet sorghum variety, Keter. In the present study, 52,928 suitable SLAF markers out of 43,528,021 pair-end reads were chosen to conduct genetic map construction, 12.0% of which were polymorphic. Among the 6353 polymorphic SLAF markers, 5829 (91.8%) were successfully genotyped in the F2mapping population. Finally 2246 SLAF markers were obtained to construct a high-density genetic linkage map. The total distance of linkage map covering all 10 chromosomes was 2158.1 cM. The largest gap on each chromosome was 10.2 cM on average. The proportion of gaps less than and/or equal to 5.0 cM was averagely 98.1%. The markers on each chromosome ranged from 123 (chromosome 9) to 315 (chromosome 4) with a mean value of 224.6, the distance between adjacent markers ranged from 0.6 (chromosome 10) to 1.3 cM (chromosome 9) with an average distance of only 0.98 cM.
  
  
  
  A high density sorghum genetic map was constructed in this study. The total length was 2158.1 cM covering all 10 chromosomes with a total number of 2246 SLAF markers. The construction of this map can provide detailed information for accurate gene localization and cloning and application of marker-assisted breeding.
authors.affiliation: Institute of Millet Crops, Hebei Academy of Agricultural & Forestry Sciences/Hebei Branch of China National Sorghum Improvement Center, Shijiazhuang, 050035, China.
authors.forename: Guisu
authors.initials: G
authors.lastname: Ji
authors.affiliation: Institute of Cereal and Oil Crops, Hebei Academy of Agricultural & Forestry Sciences, Shijiazhuang, 050035, China.
authors.forename: Qingjiang
authors.initials: Q
authors.lastname: Zhang
authors.affiliation: Institute of Millet Crops, Hebei Academy of Agricultural & Forestry Sciences/Hebei Branch of China National Sorghum Improvement Center, Shijiazhuang, 050035, China.
authors.forename: Ruiheng
authors.initials: R
authors.lastname: Du
authors.affiliation: Institute of Millet Crops, Hebei Academy of Agricultural & Forestry Sciences/Hebei Branch of China National Sorghum Improvement Center, Shijiazhuang, 050035, China.
authors.forename: Peng
authors.initials: P
authors.lastname: Lv
authors.affiliation: Institute of Millet Crops, Hebei Academy of Agricultural & Forestry Sciences/Hebei Branch of China National Sorghum Improvement Center, Shijiazhuang, 050035, China.
authors.forename: Xue
authors.initials: X
authors.lastname: Ma
authors.affiliation: Biomarker Technologies Corporation, Beijing, 101300, China.
authors.forename: Shu
authors.initials: S
authors.lastname: Fan
authors.affiliation: Institute of Millet Crops, Hebei Academy of Agricultural & Forestry Sciences/Hebei Branch of China National Sorghum Improvement Center, Shijiazhuang, 050035, China.
authors.forename: Suying
authors.initials: S
authors.lastname: Li
authors.affiliation: Institute of Millet Crops, Hebei Academy of Agricultural & Forestry Sciences/Hebei Branch of China National Sorghum Improvement Center, Shijiazhuang, 050035, China.
authors.forename: Shenglin
authors.initials: S
authors.lastname: Hou
authors.affiliation: Institute of Millet Crops, Hebei Academy of Agricultural & Forestry Sciences/Hebei Branch of China National Sorghum Improvement Center, Shijiazhuang, 050035, China.
authors.forename: Yucui
authors.initials: Y
authors.lastname: Han
authors.affiliation: Institute of Millet Crops, Hebei Academy of Agricultural & Forestry Sciences/Hebei Branch of China National Sorghum Improvement Center, Shijiazhuang, 050035, China. guoqingliu@hotmail.com.
authors.forename: Guoqing
authors.initials: G
authors.lastname: Liu
mesh_terms: D002874:Chromosome Mapping / Q000379:methods*; D059014:High-Throughput Nucleotide Sequencing; D021141:Nucleic Acid Amplification Techniques; D020641:Polymorphism, Single Nucleotide; D040641:Quantitative Trait Loci / Q000235:genetics*; D045868:Sorghum / Q000235:genetics*
keywords: High-throughput sequencing; Linkage map construction; SLAF marker; Sorghum bicolor