Development of 27 trinucleotide microsatellite markers for Saccharina japonica using next generation sequencing technology

Zhang, Linan; Peng, Jie; Li, Xiaojie; Liu, Yanling; Cui, Cuiju; Wu, Hao; Wu, Ruina; Tian, Pingping; Li, Yán

doi:10.1007/s12686-013-0089-0

Cited by 20 publications

(10 citation statements)

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“…Such findings were consistent with reports of AT/ TA being the most abundant dinucleotide repeat motif in higher plants (Kalia et al 2011). Besides mononucleotides, the trinucleotide type is most frequent in S. japonica, a result that agrees with previous reports (Zhang et al 2014a). Among trinucleotide repeat motifs, AGC/CTG is most frequent (39 %), followed by AAC/GTT (Fig.…”

Section: Resultssupporting

confidence: 93%

“…Calculated PIC values ranged from 0.08 to 0.69, and 16 loci were classified as informative markers (PIC>0.5) ( Table 2). The number of alleles in the present study was lower than in some higher plants, such as Chinese bayberry (Jiao et al 2012) and foxtail millet (Zhang et al 2014b), but similar to previously reports on S. japonica (Liu et al 2010b;Zhang et al 2014aZhang et al , 2015. Sequencing results of three SSR loci SSR marker polymorphism is mainly due to variation in SSR repeat number, which may be caused by DNA polymerase slippag e, une qual recombination, mismatch, or retrotransposition (Kalia et al 2011).…”

Section: Development Of the Ssr Markers And Polymorphic Testsupporting

confidence: 88%

“…For S. japonica, available SSRs are limited for further analysis, even though some documentation exists (Shi et al 2007;Liu et al 2010b;Zhang et al 2014aZhang et al , 2015. The limited research on S. japonica using SSR markers (Liu et al 2010a makes it desirable to develop more SSRs.…”

Section: Introductionmentioning

confidence: 99%

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Development of Saccharina japonica genomic SSR markers using next-generation sequencing

Zhang

Yao

et al. 2015

J Appl Phycol

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Illumina 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 0~0.625 and expected heterozygosities of 0.082~0.745. 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.

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Section: Resultssupporting

confidence: 93%

Section: Development Of the Ssr Markers And Polymorphic Testsupporting

confidence: 88%

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Development of Saccharina japonica genomic SSR markers using next-generation sequencing

Zhang

Yao

et al. 2015

J Appl Phycol

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“…Genomic DNA was extracted from a sporophyte blade using a Plant Genomic DNA Kit (Tiangen Biotech Co, Ltd., Beijing, China) according to the manufacturer's instructions. Fifteen polymorphic SSR primers were screened from previously published articles (Shi et al ; Liu et al ; Wang et al ; Xu et al ; Zhang et al ) and used in the genetic analysis (see Table S1 in the Supporting Information). The forward primers were labeled with fluorophores FAM at their 5′ end and polymerase chain reactions (PCRs) were performed in a total 20 μL reaction volume containing 0.5 U of the Premix Taq ( Ex Taq version, Takara, Dalian, China), 0.5 μmol/L of each primer, and 50 ng template DNA.…”

Section: Methodsmentioning

confidence: 99%

“…Applications of these markers in studies of genetic variations, marker‐assisted selection and construction of genetic linkage maps have been analyzed. With the application of multiplexing techniques and next‐generation sequencing techniques, dozens of microsatellite markers in S. japonica have been developed (Xu et al ; Zhang et al ).…”

Section: Introductionmentioning

confidence: 99%

Genetic diversity and population structure among cultivars of Saccharina japonica currently farmed in northern China

Pang

Shan

2017

Phycological Research

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Close to 50% of the annual production of the brown alga Saccharina japonica, about 2 million tons (fresh weight), is produced through farming in Shandong province, China, principally around Rongcheng. Under artificial selection for phenotypic traits (e.g. color, blade length) cultivated strains (cultivars) face the problems of inbreeding depression, which can be caused by the close relationships of the parental plants. Hence, in an attempt to evaluate genetic variations and relationships among cultivars, 15 major farmed cultivars were selected and sampled from seven major hatcheries and analyzed using 15 microsatellite markers. A total of 94 alleles were found across all samples, with allele numbers ranging from three to 17 per locus. All of the cultivars exhibited relatively high levels of genetic diversity, with mean Nei's genetic diversity (H) and the Shannon's information index (I) of 0.466 and 0.862, respectively. A UPGMA dendrogram grouped all cultivars into three main clusters. However, two of the most commonly farmed cultivars (DB and BN) from different hatcheries failed to cluster together. Instead, differently named cultivars from the same hatchery tended to group together, implying that their high similarities is partly due to the presence of genetic mixing among cultivars within a hatchery or misuse of cultivar's names. Genetic analysis performed by Bayesian model-based clustering revealed clear differentiation of three major subgroups (LJ-202 and LJ-205; LJ-C033; XS-2 and XS-BN) and one admixed group (the remaining ten cultivars). Our results revealed ambiguous genetic relationships among certain cultivars of S. japonica farmed in northern China. A more stringent and prudent regulation should be applied during breeding and production process in the future.

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Status of genetic studies and breeding of Saccharina japonica in China

et al. 2020

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Development of 27 trinucleotide microsatellite markers for Saccharina japonica using next generation sequencing technology

Cited by 20 publications

References 2 publications

Development of Saccharina japonica genomic SSR markers using next-generation sequencing

Development of Saccharina japonica genomic SSR markers using next-generation sequencing

Genetic diversity and population structure among cultivars of Saccharina japonica currently farmed in northern China

Status of genetic studies and breeding of Saccharina japonica in China

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