title: Construction of a dense genetic linkage map and mapping quantitative trait loci for economic traits of a doubled haploid population of Pyropia haitanensis (Bangiales, Rhodophyta).
abstract: BACKGROUND
  Pyropia haitanensis is one of the most economically important mariculture crops in China. A high-density genetic map has not been published yet and quantitative trait locus (QTL) mapping has not been undertaken for P. haitanensis because of a lack of sufficient molecular markers. Specific length amplified fragment sequencing (SLAF-seq) was developed recently for large-scale, high resolution de novo marker discovery and genotyping. In this study, SLAF-seq was used to obtain mass length polymorphic markers to construct a high-density genetic map for P. haitanensis.
  
  
  RESULTS
  In total, 120.33 Gb of data containing 75.21 M pair-end reads was obtained after sequencing. The average coverage for each SLAF marker was 75.50-fold in the male parent, 74.02-fold in the female parent, and 6.14-fold average in each double haploid individual. In total, 188,982 SLAFs were detected, of which 6731 were length polymorphic SLAFs that could be used to construct a genetic map. The final map included 4550 length polymorphic markers that were combined into 740 bins on five linkage groups, with a length of 874.33 cM and an average distance of 1.18 cM between adjacent bins. This map was used for QTL mapping to identify chromosomal regions associated with six economically important traits: frond length, width, thickness, fresh weight, growth rates of frond length and growth rates of fresh weight. Fifteen QTLs were identified for these traits. The value of phenotypic variance explained by an individual QTL ranged from 9.59 to 16.61 %, and the confidence interval of each QTL ranged from 0.97 cM to 16.51 cM.
  
  
  CONCLUSIONS
  The first high-density genetic linkage map for P. haitanensis was constructed, and fifteen QTLs associated with six economically important traits were identified. The results of this study not only provide a platform for gene and QTL fine mapping, map-based gene isolation, and molecular breeding for P. haitanensis, but will also serve as a reference for positioning sequence scaffolds on a physical map and will assist in the process of assembling the P. haitanensis genome sequence. This will have a positive impact on breeding programs that aim to increase the production and quality of P. haitanensis in the future.
authors.affiliation: College of Fisheries, Jimei University, Xiamen, 361021, PR China. Yanxu@jmu.edu.cn.
authors.forename: Yan
authors.initials: Y
authors.lastname: Xu
authors.affiliation: Biomarker Technologies Corporation, Beijing, 101300, PR China. huangl@biomarker.com.cn.
authors.forename: Long
authors.initials: L
authors.lastname: Huang
authors.affiliation: College of Fisheries, Jimei University, Xiamen, 361021, PR China. Dhji@jmu.edu.cn.
authors.forename: Dehua
authors.initials: D
authors.lastname: Ji
authors.affiliation: College of Fisheries, Jimei University, Xiamen, 361021, PR China. cschen@jmu.edu.cn.
authors.forename: Changsheng
authors.initials: C
authors.lastname: Chen
authors.affiliation: Biomarker Technologies Corporation, Beijing, 101300, PR China. zhenghk@biomarker.com.cn.
authors.forename: Hongkun
authors.initials: H
authors.lastname: Zheng
authors.affiliation: College of Fisheries, Jimei University, Xiamen, 361021, PR China. ctxie@jmu.edu.cn.
authors.forename: Chaotian
authors.initials: C
authors.lastname: Xie
mesh_terms: D054458:Amplified Fragment Length Polymorphism Analysis; D002681:China; D002874:Chromosome Mapping; D005819:Genetic Markers; D014644:Genetic Variation; D006238:Haploidy; D044664:Porphyra / Q000235:genetics / Q000378:metabolism; D040641:Quantitative Trait Loci; D000461:Rhodophyta / Q000235:genetics* / Q000378:metabolism
chemical_list: D005819:Genetic Markers