Genotyping-by-sequencing to determine the genetic structure of a Tibetan medicinal plant Swertia mussotii Franch.

Qiao, Yan; Guo, Fengxian; Huo, Naxin; Li, Zhan; Sun, Jiaqing; Zuo, Xixi; Guo, Zeguang; Gu, Yong; Wang, Yi; Liu, Yue

doi:10.1007/s10722-020-00993-6

Cited by 3 publications

(1 citation statement)

References 52 publications

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“…Restriction site-associated DNA (RAD) is one of the most effective genotyping-by-sequencing (GBS) methods that allow for extensive SNP discovery on the genome level ( Davey et al, 2011 ; Sonah et al, 2013 ; Puritz et al, 2014 ). It has been widely applied in population genetics for numerous model and non-model species (e.g., Wang et al, 2013 ; Luo et al, 2019 ; Feng et al, 2020 ; Xiong et al, 2020 ; Boukteb et al, 2021 ; Qiao et al, 2021 ). In particular, the UGbS-Flex (also denoted as SuperGBS) is a powerful tool for population genetic research with the ability to generate long reads (300–700 bp) and maximize SNP callings irrespective of the species ploidy level, breeding system, and reference genome availability ( Qi et al, 2018 ; Cheng et al, 2020 ).…”

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confidence: 99%

Genomic Data Reveals Profound Genetic Structure and Multiple Glacial Refugia in Lonicera oblata (Caprifoliaceae), a Threatened Montane Shrub Endemic to North China

Shen

et al. 2022

Front. Plant Sci.

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Characterizing genetic diversity and structure and identifying conservation units are both crucial for the conservation and management of threatened species. The development of high-throughput sequencing technology provides exciting opportunities for conservation genetics. Here, we employed the powerful SuperGBS method to identify 33, 758 high-quality single-nucleotide polymorphisms (SNP) from 134 individuals of a critically endangered montane shrub endemic to North China, Lonicera oblata. A low level of genetic diversity and a high degree of genetic differentiation among populations were observed based on the SNP data. Both principal component and phylogenetic analyses detected seven clusters, which correspond exactly to the seven geographic populations. Under the optimal K = 7, Admixture suggested the combination of the two small and geographically neighboring populations in the Taihang Mountains, Dongling Mountains, and Lijiazhuang, while the division of the big population of Jiankou Great Wall in the Yan Mountains into two clusters. High population genetic diversity and a large number of private alleles were detected in the four large populations, while low diversity and non-private alleles were observed for the remaining three small populations, implying the importance of these large populations as conservation units in priority. Demographic history inference suggested two drastic contractions of population size events that occurred after the Middle Pleistocene Transition and the Last Glacial Maximum, respectively. Combining our previous ecological niche modeling results with the present genomic data, there was a possible presence of glacial refugia in the Taihang and Yan Mountains, North China. This study provides valuable data for the conservation and management of L. oblata and broadens the understanding of the high biodiversity in the Taihang and Yan Mountains.

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Section: Introductionmentioning

confidence: 99%

Genomic Data Reveals Profound Genetic Structure and Multiple Glacial Refugia in Lonicera oblata (Caprifoliaceae), a Threatened Montane Shrub Endemic to North China

Shen

et al. 2022

Front. Plant Sci.

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An overview of remote monitoring methods in biodiversity conservation

Kerry

Montalbo

Das

et al. 2022

Environ Sci Pollut Res

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Conservation of biodiversity is critical for the coexistence of humans and the sustenance of other living organisms within the ecosystem. Identification and prioritization of specific regions to be conserved are impossible without proper information about the sites. Advanced monitoring agencies like the Intergovernmental Science-Policy Platform on Biodiversity and Ecosystem Services (IPBES) had accredited that the sum total of species that are now threatened with extinction is higher than ever before in the past and are progressing toward extinct at an alarming rate. Besides this, the conceptualized global responses to these crises are still inadequate and entail drastic changes. Therefore, more sophisticated monitoring and conservation techniques are required which can simultaneously cover a larger surface area within a stipulated time frame and gather a large pool of data. Hence, this study is an overview of remote monitoring methods in biodiversity conservation via a survey of evidence-based reviews and related studies, wherein the description of the application of some technology for biodiversity conservation and monitoring is highlighted. Finally, the paper also describes various transformative smart technologies like artificial intelligence (AI) and/or machine learning algorithms for enhanced working efficiency of currently available techniques that will aid remote monitoring methods in biodiversity conservation.

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Assessing SNP Heterozygosity in Potato (Solanum) Species— Bias Due to Missing and Non-allelic Genotypes

et al. 2021

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Genotyping-by-sequencing to determine the genetic structure of a Tibetan medicinal plant Swertia mussotii Franch.

Cited by 3 publications

References 52 publications

Genomic Data Reveals Profound Genetic Structure and Multiple Glacial Refugia in Lonicera oblata (Caprifoliaceae), a Threatened Montane Shrub Endemic to North China

Genomic Data Reveals Profound Genetic Structure and Multiple Glacial Refugia in Lonicera oblata (Caprifoliaceae), a Threatened Montane Shrub Endemic to North China

An overview of remote monitoring methods in biodiversity conservation

Assessing SNP Heterozygosity in Potato (Solanum) Species— Bias Due to Missing and Non-allelic Genotypes

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