title: A second generation SNP and SSR integrated linkage map and QTL mapping for the Chinese mitten crab Eriocheir sinensis.
abstract: The Chinese mitten crab Eriocheir sinensis is the most economically important cultivated crab species in China, and its genome has a high number of chromosomes (2n = 146). To obtain sufficient markers for construction of a dense genetic map for this species, we employed the recently developed specific-locus amplified fragment sequencing (SLAF-seq) method for large-scale SNPs screening and genotyping in a F1 full-sib family of 149 individuals. SLAF-seq generated 127,677 polymorphic SNP markers, of which 20,803 valid markers were assigned into five segregation types and were used together with previous SSR markers for linkage map construction. The final integrated genetic map included 17,680 SNP and 629 SSR markers on the 73 linkage groups (LG), and spanned 14,894.9 cM with an average marker interval of 0.81 cM. QTL mapping localized three significant growth-related QTL to a 1.2 cM region in LG53 as well as 146 sex-linked markers in LG48. Genome-wide QTL-association analysis further identified four growth-related QTL genes named LNX2, PAK2, FMRFamide and octopamine receptors. These genes are involved in a variety of different signaling pathways including cell proliferation and growth. The map and SNP markers described here will be a valuable resource for the E. sinensis genome project and selective breeding programs.
authors.affiliation: Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources Certified by Ministry of Education, College of Fisheries and Life Science, Shanghai Ocean University, 999 Hucheng Huan Road, Pudong New Area, Shanghai, 201306, China.
authors.forename: Gao-Feng
authors.initials: GF
authors.lastname: Qiu
authors.affiliation: Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources Certified by Ministry of Education, College of Fisheries and Life Science, Shanghai Ocean University, 999 Hucheng Huan Road, Pudong New Area, Shanghai, 201306, China.
authors.forename: Liang-Wei
authors.initials: LW
authors.lastname: Xiong
authors.affiliation: Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources Certified by Ministry of Education, College of Fisheries and Life Science, Shanghai Ocean University, 999 Hucheng Huan Road, Pudong New Area, Shanghai, 201306, China.
authors.forename: Zhi-Ke
authors.initials: ZK
authors.lastname: Han
authors.affiliation: Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources Certified by Ministry of Education, College of Fisheries and Life Science, Shanghai Ocean University, 999 Hucheng Huan Road, Pudong New Area, Shanghai, 201306, China.
authors.forename: Zhi-Qiang
authors.initials: ZQ
authors.lastname: Liu
authors.affiliation: Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources Certified by Ministry of Education, College of Fisheries and Life Science, Shanghai Ocean University, 999 Hucheng Huan Road, Pudong New Area, Shanghai, 201306, China.
authors.forename: Jian-Bin
authors.initials: JB
authors.lastname: Feng
authors.affiliation: Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources Certified by Ministry of Education, College of Fisheries and Life Science, Shanghai Ocean University, 999 Hucheng Huan Road, Pudong New Area, Shanghai, 201306, China.
authors.forename: Xu-Gan
authors.initials: XG
authors.lastname: Wu
authors.affiliation: Shanghai Fisheries Technical Extension Station, Shanghai Fisheries Research Institute, Shanghai 200433, China.
authors.forename: Yin-Long
authors.initials: YL
authors.lastname: Yan
authors.affiliation: Shanghai Mudbeach Institute of Biological Resource Exploitation, Shanghai, 202150, China.
authors.forename: Hong
authors.initials: H
authors.lastname: Shen
authors.affiliation: Biomarker Technologies Corporation, Beijing 101300, China.
authors.forename: Long
authors.initials: L
authors.lastname: Huang
authors.affiliation: Biomarker Technologies Corporation, Beijing 101300, China.
authors.forename: Li
authors.initials: L
authors.lastname: Chen
mesh_terms: D000818:Animals; D003386:Brachyura / Q000235:genetics*; D008040:Genetic Linkage; D018895:Microsatellite Repeats; D020641:Polymorphism, Single Nucleotide; D040641:Quantitative Trait Loci