Genome-Wide Microsatellites in <i>Acanthopagrus latus</i>: Development, Distribution, Characterization, and Polymorphism
Chao Peng,
Congqiang Luo,
Guangqing Xiang,
Jiezhen Huang,
Liye Shao,
Haihong Huang,
Sigang Fan
Affiliations
Chao Peng
Changde Key Innovation Team for Wetland Biology and Environmental Ecology, Hunan Provincial Key Laboratory for Molecular Immunity Technology of Aquatic Animal Diseases, College of Life and Environmental Science, Hunan University of Arts and Science, Changde 415000, China
Congqiang Luo
Changde Key Innovation Team for Wetland Biology and Environmental Ecology, Hunan Provincial Key Laboratory for Molecular Immunity Technology of Aquatic Animal Diseases, College of Life and Environmental Science, Hunan University of Arts and Science, Changde 415000, China
Guangqing Xiang
Longshan Animal Husbandry and Fisheries Affairs Center, Xiangxi 416800, China
Jiezhen Huang
Longshan Animal Husbandry and Fisheries Affairs Center, Xiangxi 416800, China
Liye Shao
Changde Key Innovation Team for Wetland Biology and Environmental Ecology, Hunan Provincial Key Laboratory for Molecular Immunity Technology of Aquatic Animal Diseases, College of Life and Environmental Science, Hunan University of Arts and Science, Changde 415000, China
Haihong Huang
Changde Key Innovation Team for Wetland Biology and Environmental Ecology, Hunan Provincial Key Laboratory for Molecular Immunity Technology of Aquatic Animal Diseases, College of Life and Environmental Science, Hunan University of Arts and Science, Changde 415000, China
Sigang Fan
Guangdong Provincial Key Laboratory of Fishery Ecology and Environment, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, China
The yellowfin seabream (Acanthopagrus latus) is an economically important commercial mariculture fish in China and Southeast Asia. Only a few simple sequence repeats (SSRs) of A. latus have been isolated and reported, which has hindered breeding progress. A total of 318,862 SSRs were isolated and characterized from the A. latus genome in this study. All SSRs were 9,069,670 bp in length, accounting for 1.32% of the genome. The density and frequency of SSRs were 468.40 loci/Mb and 13,323.19 bp/Mb, respectively. The major SSRs were dinucleotides (accounting for 76.92%), followed by trinucleotides (15.75%). The most abundant SSR motif was (AC)n (168,390, accounting for 53%), with the highest frequency (245.78 loci/Mb) and density (7304.18 bp/Mb). Most SSRs were located in non-coding regions, such as intergenic regions (34.54%) and introns (56.91%). SSR-containing exons were distributed into 51 gene ontology (GO) terms and significantly enriched in immunity- and growth-related pathways. A total of 217,791 SSR markers were successfully designed. Nine SSR markers were amplified in 29 A. latus individuals, and eight of them possess high polymorphism. The cross-species transferability of 33 out of the 37 tested loci were successfully amplified in Acanthopagrus schlegelii. These results lay the foundation for the molecular marker-assisted breeding and genetic information assessment of A. latus.
