High genetic diversity in gametophyte clones of Undaria pinnatifida from Vladivostok, Dalian and Qingdao revealed using microsatellite analysis

Shan, Tifeng; Pang, Shaojun; Feng, Liang; Xu, Na; Zhao, Xiaobo; Gao, Shaopeng

doi:10.1007/s00343-012-1098-7

Cited by 5 publications

(3 citation statements)

References 19 publications

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“…Fortunately, five SLAF and one SSR markers were found to be completely linked to sex trait in this study, therefore these markers will be of special importance in characterizing the structure of the sex determining region (SDR). In previous studies, the SSR marker (UP-AC-2A8) has been identified to be tightly linked to quite a number of female gametophytes that were originated from geographically isolated populations [ 43 , 44 , 52 ]. This study further confirmed the sex linked characteristics of this marker in a segregating family.…”

Section: Discussionmentioning

confidence: 99%

Construction of a high-density genetic map and mapping of a sex-linked locus for the brown alga Undaria pinnatifida (Phaeophyceae) based on large scale marker development by specific length amplified fragment (SLAF) sequencing

Shan

Pang

et al. 2015

BMC Genomics

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BackgroundUndaria pinnatifida is an important economic brown alga in East Asian countries. However, its genetic and genomic information is very scarce, which hinders further research in this species. A high-density genetic map is a basic tool for fundamental and applied research such as discovery of functional genes and mapping of quantitative trait loci (QTL). In this study the recently developed specific length amplified fragment sequencing (SLAF-seq) technology was employed to construct a high-density genetic linkage map and locate a sex determining locus for U. pinnatifida.ResultsA total of 28.06 Gb data including 140.31 M pair-end reads was obtained. After linkage analysis 4626 SLAF markers were mapped onto the genetic map. After adding the sex linked simple sequence repeat (SSR) marker [GenBank:AY738602.1], the final genetic map was 1816.28 cM long, consisting of 30 linkage groups with an average distance of 0.39 cM between adjacent markers. The length of LGs ranged from 20.12 to 106.95 cM. A major sex associated QTL was mapped to LG22 within a window starting at 29.01 cM and ending at 68.81 cM with a total of 68 SLAF markers. The SSR marker and five SLAF markers (Marker6556, 19020, 43089, 60771 and 26359) were identified as tightly sex-linked markers, as indicated by the absence of recombination between them and the sex phenotype. These markers were located at the position of 59.50 cM, which was supposed to be the sex determining region.ConclusionsA high-density genetic linkage map was constructed using SLAF-seq technique and F1 gametophyte population for the first time in the economically important brown alga U. pinnatifida. For the first time, a major sex associated QTL suggesting a sex determining region was mapped to a single LG. This map will facilitate the further fundamental and applied research such as QTL mapping and map-based gene clone in U. pinnatifida and provide a reference for studies in other kelp species.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-2184-y) contains supplementary material, which is available to authorized users.

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Section: Discussionmentioning

confidence: 99%

Construction of a high-density genetic map and mapping of a sex-linked locus for the brown alga Undaria pinnatifida (Phaeophyceae) based on large scale marker development by specific length amplified fragment (SLAF) sequencing

Shan

Pang

et al. 2015

BMC Genomics

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“…Significant and strong population structure is typically present among kelp populations (Billot, Engel, Rousvoal, Kloareg, & Valero, 2003;Johansson et al, 2015;Uwai et al, 2006). However, low levels of population structure have been documented for regions with strong boundary currents (Coleman et al, 2011), populations resulting from human-mediated invasion events (Grulois, Leveque, & Viard, 2011), and natural ranges with high levels of cultivation and/or transport activities (Shan et al, 2012;Zhang et al, 2015). Therefore, it is important to document the undisturbed genomic variation in a kelp taxon prior to its exploitation.…”

Section: Introductionmentioning

confidence: 99%

Strong population structure but no equilibrium yet: Genetic connectivity and phylogeography in the kelp Saccharina latissima (Laminariales, Phaeophyta)

Luttikhuizen

Heuvel

Rebours

et al. 2018

Ecology and Evolution

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Kelp aquaculture is globally developing steadily as human food source, along with other applications. One of the newer crop species is Saccharina latissima, a northern hemisphere kelp inhabiting temperate to arctic rocky shores. To protect and document its natural genetic variation at the onset of this novel aquaculture, as well as increase knowledge on its taxonomy and phylogeography, we collected new genetic data, both nuclear and mitochondrial, and combined it with previous knowledge to estimate genetic connectivity and infer colonization history. Isolation‐with‐migration coalescent analyses demonstrate that gene flow among the sampled locations is virtually nonexistent. An updated scenario for the origin and colonization history of S. latissima is developed as follows: We propose that the species (or species complex) originated in the northwest Pacific, crossed to the northeast Pacific in the Miocene, and then crossed the Bering Strait after its opening ~5.5 Ma into the Arctic and northeast Atlantic. It subsequently crossed the Atlantic from east to west. During the Pleistocene, it was compressed in the south with evidence for northern refugia in Europe. Postglacial recolonization led to secondary contact in the Canadian Arctic. Saccharina cichorioides is shown to probably belong to the S. latissima species complex and to derive from ancestral populations in the Asian North Pacific. Our novel approach of comparing inferred gene flow based on coalescent analysis versus Wright's island model suggests that equilibrium levels of differentiation have not yet been reached in Europe and, hence, that genetic differentiation is expected to increase further if populations are left undisturbed.

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“…However, DNA sequences revealed a low population genetic differentiation within 21 localities in Japan (Uwai et al 2006a), possibly due to wide‐ranging introductions of cultivated strains between one another for mariculture purposes since the 1960s (Ohno et al 1999). In contrast, genetic analyses based on polymorphic microsatellites revealed a high genetic diversity within the natural and farmed populations from China (Shan et al 2012, 2018; Li et al 2020). Li et al (2013) found that around 64% genetic variation occurred amongst populations and 36% occurred within the populations.…”

Section: Dna Fingerprinting and Genetic Assessmentmentioning

confidence: 99%

Kelp aquaculture in China: a retrospective and future prospects

Shan

Zhang

et al. 2021

Reviews in Aquaculture

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Globally, China has the largest scale of kelp cultivation and production operations. However, its kelp aquaculture industry is suffering from declining germplasm diversity, degradation of agronomic traits, the presence of polluted environments, changing ocean conditions and increasing anthropological interference. This review covers two of the most commercially important kelp species in China, viz. Saccharina japonica and Undaria pinnatifida. It summarizes the history of their cultivation, production, economic and ecological benefits, their breeding programmes (e.g. inter-and intra-specific hybridization and marker-assisted selection) and efforts towards population genetic diversity and conservation. The article focuses on three significant challenges, for example genetic crosscontamination between the wild and farmed kelp populations, ocean warming and ocean acidification. Accordingly, we outline the steps required to provide several intervention measures, for example (i) collection and preservation of wild and cultivated kelp germplasm; (ii) selection of suitable cultivation sites under changing environmental conditions; (iii) developing stress-resistant cultivars; and finally, (iv) adoption of innovative cultivation models. The review concludes with genome-based, designs for molecular breeding and calls for the establishment of an East Asian Kelp Consortium (EAKC). Collectively, the Chinese kelp industry could provide beneficial goods and services, for example bioenergy to fine chemicals and environmental benefits, such as carbon capture, pH amelioration and provision of habitat for many other marine species of commercial value. The strategies proposed in this article thus have the potential to not only improve but also reinvigorate the kelp industry in China and nearby Japan and Korea, in the context of both environmental health and economic benefits.

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High genetic diversity in gametophyte clones of Undaria pinnatifida from Vladivostok, Dalian and Qingdao revealed using microsatellite analysis

Cited by 5 publications

References 19 publications

Construction of a high-density genetic map and mapping of a sex-linked locus for the brown alga Undaria pinnatifida (Phaeophyceae) based on large scale marker development by specific length amplified fragment (SLAF) sequencing

Construction of a high-density genetic map and mapping of a sex-linked locus for the brown alga Undaria pinnatifida (Phaeophyceae) based on large scale marker development by specific length amplified fragment (SLAF) sequencing

Strong population structure but no equilibrium yet: Genetic connectivity and phylogeography in the kelp Saccharina latissima (Laminariales, Phaeophyta)

Kelp aquaculture in China: a retrospective and future prospects

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