Development and characterization of microsatellite markers from an enriched genomic library of Saccharina japonica

Zhang, Jing; Li, Wei; Qu, Jing; Wang, Xumin; Liu, Cui; Liu, Tao

doi:10.1007/s10811-014-0301-y

Cited by 17 publications

(6 citation statements)

References 40 publications

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“…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%

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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: 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%

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

Zhang

Yao

et al. 2015

J Appl Phycol

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“…However, the previous genetic linkage map of Saccharina mainly focused on AFLP markers and only a few SSR markers were available [ 17 – 20 ] because developing SSR involved time-consuming and labor-intensive [ 50 ]. For the construction of a high-density genetic linkage map, we have constructed the Saccharina SSR enriched genomic library and developed SSR markers on a large scale [ 30 ]. In this work, 37 AFLP markers with 221 polymorphic loci, 22 SRAP markers with 133 polymorphic loci and 139 SSR markers with 278 polymorphic loci were screened.…”

Section: Discussionmentioning

confidence: 99%

“…60 SSR primers from Billot et al [ 26 ], Liu et al [ 27 ], Shi et al [ 28 ] and Wang et al [ 29 ] were selected in this study firstly. Then together with 266 our newly developed SSR primers from the (AC) n enriched genomic library [ 30 ], a total of 326 primers were synthesized at Invitrogen, Shanghai, China. The PCR was performed under the following conditions: 5 min at 95°C, then 35 cycles of 1 min at 92°C, 1 min at appropriate annealing temperature, and 1 min at 72°C, and a final extension step of 10 min at 72°C.…”

Section: Methodsmentioning

confidence: 99%

Genetic Map Construction and Quantitative Trait Locus (QTL) Detection of Six Economic Traits Using an F2 Population of the Hybrid from Saccharina longissima and Saccharina japonica

et al. 2015

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Saccharina (Laminaria) is one of the most important economic seaweeds. Previously, four genetic linkage maps of Saccharina have been constructed and five QTLs have been identified. However, they were not enough for its breeding. In this work, Saccharina longissima (♀) and Saccharina japonica (♂), which showed obvious differences in morphology and genetics, were applied in hybridization to yield the F2 mapping population with 102 individuals. Using these 102 F2 hybrids, the genetic linkage map of Saccharina was constructed by MapMaker software based on 37 amplified fragment length polymorphisms (AFLPs), 22 sequence-related amplified polymorphisms (SRAPs) and 139 simple sequence repeats (SSRs) markers. Meanwhile, QTL analysis was performed for six economic traits. The linkage map constructed in this research consisted of 422 marker loci (137 AFLPs, 57 SRAPs and 228 SSRs), which formed 45 linkage groups (LGs) with an average marker space of 7.92 cM; they spanned a total length of 2233.1 cM, covering the whole estimated genome size. A total of 29 QTLs were identified for six economic traits, which explained 1.06 to 64.00% of phenotypic variation, including three QTLs for frond length (FL) and raw weight (RW), five QTLs for frond width (FW), two QTLs for frond fascia width (FFW) and frond thickness (FT), and fourteen QTLs for base shape (BS). The results of this research will improve the breeding efficiency and be beneficial for marker-assisted selection (MAS) schemes in Saccharina breeding.

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“…The ability to effectively transfer microsatellite markers across taxa has been successfully demonstrated in many species (see for review in plants: Ellis and Burke 2007;in animals: Hutter et al 1998 andin kelps: Liu et al 2012;Coelho et al 2014;Zhang et al 2015). The results of many studies have clearly indicated that EST-derived microsatellite markers have a higher transfer rate compared to those developed from anonymous nuclear DNA regions, due to greater DNA sequence conservation in transcribed versus non-coding regions.…”

Section: Characteristics Of Microsatellites and Transferability Between Speciesmentioning

confidence: 99%

Development of tools to rapidly identify cryptic species and characterize their genetic diversity in different European kelp species

et al. 2021

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Marine ecosystems formed by kelp forests are severely threatened by global change and local coastline disturbances in many regions. In order to take appropriate conservation, mitigation and restoration actions, it is crucial to identify the most diverse populations which could serve as a "reservoir" of genetic diversity. This requires the development of specific tools, such as microsatellite markers to investigate the level and spatial distribution of genetic diversity. Here, we tested new polymorphic microsatellite loci from the genome of the kelp, Laminaria digitata, and tested them for cross-amplification and polymorphism in four closely related congeneric species (Laminaria hyperborea, Laminaria ochroleuca, Laminaria rodriguezii and Laminaria pallida). Adding these 20 new microsatellite loci to the ten L. digitata loci previously developed by Billot et al. (1998) and Brenan et al. (2014) and to the ten L. ochroleuca loci previously developed by Coelho et al. (2014), we retained a total of 30 polymorphic loci for L. digitata, 21 for L. hyperborea, 16 for L ochroleuca, 18 for L. rodriguezii and 12 for L.pallida. These markers have been tested for the first time in the last two species. As predicted, the proportion of markers that cross-amplified between species decreased with increasing genetic distance. In addition, as problems of species identification were reported in this family, mainly between L. digitata and Hedophyllum nigripes, but also between L. digitata, L. hyperborea and L. ochroleuca in areas where their range distributions overlap, we report a rapid PCR identification method based on species-specific COI mitochondrial primers that allows these four species of kelp to be rapidly distinguished.

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Development and characterization of microsatellite markers from an enriched genomic library of Saccharina japonica

Cited by 17 publications

References 40 publications

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

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

Genetic Map Construction and Quantitative Trait Locus (QTL) Detection of Six Economic Traits Using an F2 Population of the Hybrid from Saccharina longissima and Saccharina japonica

Development of tools to rapidly identify cryptic species and characterize their genetic diversity in different European kelp species

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