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Development of Saccharina japonica genomic SSR markers using next-generation sequencing
Li, Qiuying1,2; Zhang, Jie1,2; Yao, Jianting1; Wang, Xiuliang1; Duan, Delin1
2016-04-01
Source PublicationJOURNAL OF APPLIED PHYCOLOGY
Volume28Issue:2Pages:1387-1390
SubtypeArticle
AbstractIllumina HiSeq 2000 next-generation sequencing (NGS) was used on Saccharina japonica specimens to develop SSRs from high-quality genomic sequences. There were 181,595 SSR loci identified using the MISA program. SSR repeat types are plentiful in genomic sequences of S. japonica, with the most abundant types being mononucleotides (54 %) and trinucleotides (26 %). Six hundred primer pairs were selected and synthesized from 19,658 primer pairs, showing 166 polymorphic SSR loci (28 %) in three selected S. japonica individuals. Sixty polymorphic SSRs were further analyzed in 24 S. japonica individuals, showing two to seven alleles for each locus (average 3.7 alleles), with observed heterozygosities of 0 similar to 0.625 and expected heterozygosities of 0.082 similar to 0.745. Polymorphism information content (PIC) values ranged from 0.08 to 0.69. Sixteen loci were classified as informative markers (PIC > 0.5). Polymorphic SSR markers developed in this study should be useful for examining genetic diversity, assessment of population structure, QTL mapping, and marker-assisted selection in S. japonica.
KeywordMicrosatellite Saccharina Japonica Simple Sequence Repeats Phaeophyta
DOI10.1007/s10811-015-0643-0
Indexed BySCI
Language英语
WOS IDWOS:000372256900067
Citation statistics
Cited Times:5[WOS]   [WOS Record]     [Related Records in WOS]
Document Type期刊论文
Identifierhttp://ir.qdio.ac.cn/handle/337002/126208
Collection实验海洋生物学重点实验室
Affiliation1.Chinese Acad Sci, Inst Oceanol, Key Lab Expt Marine Biol, Qingdao 266071, Peoples R China
2.Univ Chinese Acad Sci, Beijing 100049, Peoples R China
First Author AffilicationKey Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences
Recommended Citation
GB/T 7714
Li, Qiuying,Zhang, Jie,Yao, Jianting,et al. Development of Saccharina japonica genomic SSR markers using next-generation sequencing[J]. JOURNAL OF APPLIED PHYCOLOGY,2016,28(2):1387-1390.
APA Li, Qiuying,Zhang, Jie,Yao, Jianting,Wang, Xiuliang,&Duan, Delin.(2016).Development of Saccharina japonica genomic SSR markers using next-generation sequencing.JOURNAL OF APPLIED PHYCOLOGY,28(2),1387-1390.
MLA Li, Qiuying,et al."Development of Saccharina japonica genomic SSR markers using next-generation sequencing".JOURNAL OF APPLIED PHYCOLOGY 28.2(2016):1387-1390.
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