Genetic diversity and population structure of <i>Quercus fabri</i> Hance in China revealed by genotyping‐by‐sequencing

Xiong, Shifa; Zhao, Yi; Chen, Yicun; Gao, Ming; Wu, Liwen; Wang, Yangdong

doi:10.1002/ece3.6598

Cited by 10 publications

(5 citation statements)

References 28 publications

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“…The Quercus plant genus plays an important role in water conservation, soil and water conservation and ecological stability [ 31 ]. Quercus fabri Hance, Quercus serrata Thunb, Quercus acutissima Carruth and Quercus variabilis Bl are the dominant species in deciduous broad-leaved forests and mixed coniferous forests in temperate and warm temperate regions of China and are also the forest building blocks in most parts of the country [ 32 , 33 ]. Oak tree wood is dense and beautifully textured, resistant to wear and decay and is often used as a high-quality material for building and household purposes [ 34 ].…”

Section: Introductionmentioning

confidence: 99%

Effects of Drought Stress and Rehydration on Physiological and Biochemical Properties of Four Oak Species in China

Xiong

Wang

Chen

et al. 2022

Plants

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Quercus fabri Hance, Quercus serrata Thunb, Quercus acutissima Carruth, and Quercus variabilis BL are four Chinese oak species commonly used for forestation. To ensure the survival of seedlings, we first need to understand the differences in drought resistance of the four oak species at the seedling stage, and comprehensively evaluate their drought resistance capabilities. The four oak seedlings were divided into drought-rewatering treatment group and well watered samples (control group). For the seedlings of the drought-rewatering treatment group, drought stress lasting 31 days was used, and then re-watering for 5 days. The water parameters, osmotic solutes content, antioxidant enzyme activity and photosynthesis parameters of the seedlings in the two groups were measured every 5 days. Compared with the control group, the relative water content, water potential, net photosynthetic rate, transpiration rate, and stomatal conductance levels of the four oaks all showed a downward trend under continuous drought stress, and showed an upward trend after rehydration. The soluble protein, soluble sugar, proline, peroxidase, superoxide dismutase and catalase content of the four oaks increased first and then decreased under drought stress, and then increased after rehydration. The content of glycine betaine and malondialdehyde continued to increase, and gradually decreased after rehydration. The weight of each index was calculated by principal component analysis, and then the comprehensive evaluation of each index was carried out through the membership function method. The drought resistance levels of the four oak species were as follows: Q. serrata > Q. fabri > Q. variabilis > Q. acutissima.

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Section: Introductionmentioning

confidence: 99%

Effects of Drought Stress and Rehydration on Physiological and Biochemical Properties of Four Oak Species in China

Xiong

Wang

Chen

et al. 2022

Plants

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“…), flowering dogwood ( C. florida ), and oak ( Quercus spp.) (Li et al., 2023 ; Pais et al., 2020 ; Xiong et al., 2020 ). In the study reported here, we document the first population genetic analysis of S. ovata populations in the Cumberland Plateau and Great Smoky Mountain region of the southern United States achieved using a GBS approach (Narum et al., 2013 ).…”

Section: Discussionmentioning

confidence: 99%

“…), flowering dogwood (C. florida), and oak (Quercus spp.) (Li et al, 2023;Pais et al, 2020;Xiong et al, 2020).…”

Section: Discussionmentioning

confidence: 99%

Genetic diversity and population structure of a rare flowering tree endemic to Appalachia, Stewartia ovata

Yadav,

Bellis,

Smith

et al. 2024

Ecology and Evolution

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Stewartia ovata (cav.) Weatherby, commonly known as mountain stewartia, is an understory tree native to the southeastern United States (U.S.). This relatively rare species occurs in isolated populations in Virginia, Kentucky, Tennessee, North Carolina, South Carolina, Georgia, Alabama, and Mississippi. As a species, S. ovata has largely been overlooked, and limited information is available regarding its ecology, which presents obstacles to conservation efforts. Stewartia ovata has vibrant, large white flowers that bloom in summer with a variety of filament colors, suggesting potential horticultural traits prized by ornamental industry. However, S. ovata is relatively slow growing and, due to long seed dormancy, propagation is challenging with limited success rates. This has created a need to assess the present genetic diversity in S. ovata populations to inform potential conservation and restoration of the species. Here, we employ a genotyping‐by‐sequencing (GBS) approach to characterize the spatial distribution and genetic diversity of S. ovata in the southern Appalachia region of the eastern United States. A total of 4475 single nucleotide polymorphisms (SNPs) were identified across 147 individuals from 11 collection sites. Our results indicate low genetic diversity (He = 0.216), the presence of population structure (K = 2), limited differentiation (FST = 0.039), and high gene flow (Nm = 6.16) between our subpopulations. Principal component analysis corroborated the findings of STRUCTURE, confirming the presence of two distinct S. ovata subpopulations. One subpopulation mainly contains genotypes from the Cumberland Plateau, Tennessee, while the other consists of genotypes present in the Great Smoky Mountain ranges in Tennessee, North Carolina, and portions of Nantahala, Chattahoochee‐Oconee national forests in Georgia, highlighting that elevation likely plays a major role in its distribution. Our results further suggested low inbreeding coefficient (FIS = 0.070), which is expected with an outcrossing tree species. This research further provides necessary insight into extant subpopulations and has generated valuable resources needed for conservation efforts of S. ovata.

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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 ).…”

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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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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Genetic diversity and population structure of Quercus fabri Hance in China revealed by genotyping‐by‐sequencing

Cited by 10 publications

References 28 publications

Effects of Drought Stress and Rehydration on Physiological and Biochemical Properties of Four Oak Species in China

Effects of Drought Stress and Rehydration on Physiological and Biochemical Properties of Four Oak Species in China

Genetic diversity and population structure of a rare flowering tree endemic to Appalachia, Stewartia ovata

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

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