EST‐SSR‐based landscape genetics of<i>Pseudotaxus chienii</i>, a tertiary relict conifer endemic to China

Li, Shufeng; Wang, Zhen; Su, Yingjuan; Wang, Ting

doi:10.1002/ece3.7769

Cited by 11 publications

(14 citation statements)

References 121 publications

(154 reference statements)

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“…Genetic diversity is an important indicator in the conservation and management of plant genetic resources ( Chen et al, 2018 ).In this study, genetic parameters were detected in 134 individuals by the 28 EST-SSRs. The mean PIC value was 0.345, indicating a mean level of genetic information, and similar results were observed in C. japonica (0.325) ( Ueno et al, 2012 ), A. argotaenia (0.455) ( Ruan et al, 2019 ), and P. koraiensis (0.404) ( Li et al, 2021 ). Mean A (4.214) was higher than that reported for T. grandis (2.636) ( Zeng et al, 2018 ) and L. principis-rupprechtii (3.850) ( Dong et al, 2018 ), but lower than that for P. koraiensis (6.45) ( Li et al, 2020 ) and P. chienii (6.4) ( Xu et al, 2020 ).…”

Section: Discussionsupporting

confidence: 77%

“…In this study, a total of 36446 unigenes were used to detect SSRs, and finally 4352 unigenes containing 5089 SSRs were identified. The distribution frequency was 11.94%, which was similar to that of C. hainanensis (11.39%) ( Qiao et al, 2014 ) and P. chienii (11.15%) ( Xu et al, 2020 ), higher than that of P. bungeana (9.21%) ( Duan et al, 2017 ), Torreya grandis (2.75%) ( Zeng et al, 2018 ), A. argotaenia (7.68%) ( Ruan et al, 2019 ), and P. koraiensis (6.84%) ( Li et al, 2021 ), lower than that of Lycium barbarum (27.93%) ( Chen et al, 2017 ), Dalbergia odorifera (23.31%) ( Liu et al, 2019 ), and peony (20.38%) ( He et al, 2020 ). The average density of SSRs was 1/11.1 kb, lower than that of C. hainanensis (1/8.08 kb) ( Qiao et al, 2014 ), Glyptostrobus pensilis (1/7.59 kb) ( Li et al, 2019 ), and P. chienii (1/9.18 kb) ( Xu et al, 2020 ), while higher than that in P. dabeshanensis (1/23.08 kb) ( Xiang et al, 2015 ), P. koraiensis (1/17.38 kb) ( Du et al, 2017 ), and L. principis-rupprechtii (1/26.8 kb) ( Dong et al, 2018 ).…”

Section: Discussionmentioning

confidence: 58%

“… Zeng et al (2018) developed 11 EST-SSRs of T. grandis , which revealed a moderate level of genetic diversity and two different genetic groups within this species. Li et al (2021) also investigated the genetic variation and population structure of 20 EST-SSRs. All these studies proved that EST-SSRs are effective molecular markers for studying the genetic diversity of conifers with high transferability.…”

Section: Introductionmentioning

confidence: 99%

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Development and Application of EST-SSR Markers in Cephalotaxus oliveri From Transcriptome Sequences

et al. 2021

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Cephalotaxus oliveri is an endemic conifer of China, which has medicinal and ornamental value. However, the limited molecular markers and genetic information are insufficient for further genetic studies of this species. In this study, we characterized and developed the EST-SSRs from transcriptome sequences for the first time. The results showed that a total of 5089 SSRs were identified from 36446 unigenes with a density of one SSR per 11.1 kb. The most common type was trinucleotide repeats, excluding mononucleotide repeats, followed by dinucleotide repeats. AAG/CTT and AT/AT exhibited the highest frequency in the trinucleotide and dinucleotide repeats, respectively. Of the identified SSRs, 671, 1125, and 1958 SSRs were located in CDS, 3′UTR, and 5′UTR, respectively. Functional annotation showed that the SSR-containing unigenes were involved in growth and development with various biological functions. Among successfully designed primer pairs, 238 primer pairs were randomly selected for amplification and validation of EST-SSR markers and 47 primer pairs were identified as polymorphic. Finally, 28 high-polymorphic primers were used for genetic analysis and revealed a moderate level of genetic diversity. Seven natural C. oliveri sampling sites were divided into two genetic groups. Furthermore, the 28 EST-SSRs had 96.43, 71.43, and 78.57% of transferability rate in Cephalotaxus fortune, Ametotaxus argotaenia, and Pseudotaxus chienii, respectively. These markers developed in this study lay the foundation for further genetic and adaptive evolution studies in C. oliveri and related species.

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Section: Discussionsupporting

confidence: 77%

Section: Discussionmentioning

confidence: 58%

Section: Introductionmentioning

confidence: 99%

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Development and Application of EST-SSR Markers in Cephalotaxus oliveri From Transcriptome Sequences

et al. 2021

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“…Genetic diversity is an important indicator in the conservation and management of plant genetic resources (Chen et al, 2018).In this study, genetic parameters were detected in 134 individuals by the 28 EST-SSRs. The mean PIC value was 0.345, indicating a mean level of genetic information, and similar results were observed in C. japonica (0.325) (Ueno et al, 2012), A. argotaenia (0.455) (Ruan et al, 2019), and P. koraiensis (0.404) (Li et al, 2021). Mean A (4.214) was higher than that reported for T. grandis (2.636) (Zeng et al, 2018) and L. principis-rupprechtii (3.850) (Dong et al, 2018), but lower than that for P. koraiensis (6.45) and P. chienii (6.4) (Xu et al, 2020).…”

Section: Discussionsupporting

confidence: 78%

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“…Landscape and environmental characteristics influence population genetic differentiation and spatial genetic structure (Li et al 2021). Given the sessile life form of plants, pollen and seed dispersal account for gene flow within and among populations, depending on habitat preferences and dispersal vectors (Cruzan et al 2020).…”

Section: Introductionmentioning

confidence: 99%

Spatial genetic structure of two conifers in a highly modified landscape of central Mexico

Cruz-Salazar

Flores‐Manzanero

2023

Preprint

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Forests have been globally reduced due to unprecedented rates of deforestation and habitat transformation, which in turn affects the species’ genetic structure. Despite harboring a high endemism, temperate forests are the second most degraded terrestrial ecosystem in Mexico. Therefore, understanding the spatial genetic patterns is fundamental to implement management and conservation efforts that contribute with their long-term persistence. By using Single Nucleotide Polymorphisms, this study evaluated the fine-scale spatial genetic structure and the effect of landscape features on gene flow of two conifers, Abies religiosa and Pinus montezumae, each with different successional affinity, in a temperate forest of central Mexico exhibiting high landscape heterogeneity due to topography and land-use changes. Based on successional affinity of species we expected isolation by resistance in Abies religiosa and a panmictic population in Pinus montezumae. We analyzed the genetic structure and the effects of altitude, Aspect and land-use changes on the genetic connectivity patterns. A weak isolation by distance pattern was detected in A. religiosa, while the spatial component explained only the 3% of its genetic variation. In P. montezumae, a very low structure signal was detected between slopes. Overall, the analyses revealed an absence of genetic structure in both species, i.e., no landscape predictor had an effect on gene flow between the populations. We recommend increasing the spatial extent and the assessment of more environmental predictors to further support the study of genetic structure patterns in the species studied. Our study contributes with information for the conservation of Mexican temperate forests.

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EST‐SSR‐based landscape genetics ofPseudotaxus chienii, a tertiary relict conifer endemic to China

Cited by 11 publications

References 121 publications

Development and Application of EST-SSR Markers in Cephalotaxus oliveri From Transcriptome Sequences

Development and Application of EST-SSR Markers in Cephalotaxus oliveri From Transcriptome Sequences

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Spatial genetic structure of two conifers in a highly modified landscape of central Mexico

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