Linking Ecology to Genetics to Better Understand Adaptation and Evolution: A Review in Marine Macrophytes

Hu, Zi‐Min; Zhong, Kai-Le; Weinberger, Florian; Duan, Delin; Draisma, Stefano G. A.; Serrão, Ester A.

doi:10.3389/fmars.2020.545102

Cited by 18 publications

(10 citation statements)

References 120 publications

(160 reference statements)

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“…Furthermore, the regulatory gene network underlying fucoidan and alginate biosynthesis also has broad applications for genetic breeding and improvement. The integration of ecology and genetics can help us to better understand how cultivated kelps acclimate and adapt to changing environments (Hu et al 2020).…”

Section: Discussionmentioning

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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Section: Discussionmentioning

confidence: 99%

Kelp aquaculture in China: a retrospective and future prospects

Shan

Zhang

et al. 2021

Reviews in Aquaculture

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“…Genomic characterization of freshwater plants has been hampered by biological and technical challenges, plus biases in scientific research (Matheson & McGaughran, 2022;Troudet et al, 2017). Hundreds to thousands of molecular markers are often required for genomic-based research on topics such as gene flow and adaptation of non-model organisms (da Fonseca et al, 2016;Stapley et al, 2010), but the de novo development of genomic resources can be both time-consuming and expensive (Hu et al, 2020;Ortega et al, 2020;Prieto et al, 2021). Overcoming these challenges is feasible with novel, rapid and costeffective methods that capture genome-wide genetic variation, allowing researchers to address questions related to taxonomy, evolution, and conservation (Andrews et al, 2016;Goodwin et al, 2016).…”

Section: Introductionmentioning

confidence: 99%

Development of genomic resources for cattails (Typha), a globally important macrophyte genus

Aleman

Dorken

Shafer

et al. 2023

Preprint

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A critical knowledge gap in freshwater plants research is the lack of genetic resources necessary to answer fundamental questions about their demographic histories, adaptation, and taxonomy. One example of this isTypha, a macrophyte genus essential to wetlands that is also becoming an increasingly problematic biological invader in numerous regions worldwide; while important insights have been discovered for this genus, currently available genetic markers are insufficient to resolve its phylogenetic relationships, population structure, and hybridization dynamics. We performed a cost and time-accessible library preparation for high-throughput sequencing to develop a suite of genomic resources forTypha. Genome-wide nuclear SNPs of 140Typhasamples from North America, temperate Eurasia and Africa revealed three independent genetic clusters corresponding toT. angustifolia,T. domingensisandT. latifolia. Data from ~40% of the nuclear genome was obtained, permitting the characterization of 119,324 nuclear diagnostic markers (SNPs that differentiate the three species). A reference-guided workflow to reconstruct whole-chloroplast-genome sequences was implemented, recovering ~60% of the genome per sample. Three genetic lineages were identified from the cpDNA phylogenetic analysis, agreeing with those determined from nrDNA. With a cost below 15 USD per sample and a processing time of two hours for the library preparation, this is a rapid and cost-effective protocol for population genomic studies. The genomic locations of diagnostic markers and the chloroplast sequences produced in this study will be permanent resources that can be incorporated into future studies ofTypha, a globally important and evolutionarily dynamic genus.

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“…Genetic characterisation of freshwater plants has been hampered by biological and technical challenges, plus biases in scientific research (Matheson & McGaughran, 2022; Troudet et al., 2017). Hundreds to thousands of molecular markers are often required for genomic‐based research on topics such as gene flow and adaptation of non‐model organisms (da Fonseca et al., 2016; Stapley et al., 2010), but the de novo development of genomic resources can be both time‐consuming and expensive (Hu et al., 2020; Ortega et al., 2020; Prieto et al., 2021). Overcoming these challenges is now feasible using novel, rapid and cost‐effective methods that capture genome‐wide genetic variation, allowing researchers to address questions related to taxonomy, evolution and conservation (Andrews et al., 2016; Goodwin et al., 2016).…”

Section: Introductionmentioning

confidence: 99%

Development of genomic resources for cattails (Typha), a globally important macrophyte genus

Aleman,

Dorken,

Shafer

et al. 2023

Freshwater Biology

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A critical knowledge gap in freshwater plant research is the lack of genetic tools necessary to answer fundamental questions about their demographic histories, adaptation and phylogenetic relationships. One example of this is Typha, a global genus of freshwater plants foundational to wetlands that also is becoming an increasingly problematic biological invader in numerous regions worldwide; although important insights have been discovered for this genus, existing markers are insufficient to answer fundamental questions about their demographic histories, adaptation and phylogenetic relationships; to identify introduced and hybrid lineages; and to examine patterns of hybridisation and introgression. We optimised a library preparation and data processing protocol to develop genome–wide nuclear and plastid resources for studying the evolutionary history, genetic structure and diversity, hybridisation, local adaptation, invasiveness, and geographical expansion dynamics of Typha. We sequenced 140 Typha samples and identified ~120 K nuclear single nucleotide polymorphisms (SNPs) that differentiate T. angustifolia, T. domingensis and T. latifolia, and retrieved their plastome sequences. We observed genetic introgression among the three species. Following a fast, straightforward and cost‐efficient genomic library preparation protocol, we produced a suite of genome‐wide resources to facilitate investigations into the taxonomy and population genetics of Typha and to advance the genomic understanding of wetland plants. The protocol described, the updated chromosome‐level genome assembly of T. latifolia, the catalogue of species‐specific SNPs, and the chloroplast sequences produced in this study comprise permanent resources that can be applied to study the genetic composition of multiple populations and hybrid zones, and will be incorporated into future studies of Typha, an ecologically important and globally invasive macrophyte.

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Linking Ecology to Genetics to Better Understand Adaptation and Evolution: A Review in Marine Macrophytes

Cited by 18 publications

References 120 publications

Kelp aquaculture in China: a retrospective and future prospects

Kelp aquaculture in China: a retrospective and future prospects

Development of genomic resources for cattails (Typha), a globally important macrophyte genus

Development of genomic resources for cattails (Typha), a globally important macrophyte genus

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