Genetic Diversity and Population Structure of an Arctic Tertiary Relict Tree Endemic to China (<i>Sassafras tzumu</i>) Revealed by Novel Nuclear Microsatellite (nSSR) Markers
<i>Sassafras tzumu</i> (Hemsl.) Hemsl., as an Arctic Tertiary relict woody species, is an ecologically and economically important deciduous tree endemic to southern China. Nonetheless, the genetic resources and backgrounds of <i>S. tzumu</i> are still lacking and remain large...
| Main Authors: | , , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
MDPI AG
2022-10-01
|
| Series: | Plants |
| Subjects: | |
| Online Access: | https://www.mdpi.com/2223-7747/11/20/2706 |
| _version_ | 1797470196544307200 |
|---|---|
| author | Shuang Wang Ying Wang Jingbo Zhou Pan Li Hungwei Lin Ye Peng Lipeng Yu Yunyan Zhang Zhongsheng Wang |
| author_facet | Shuang Wang Ying Wang Jingbo Zhou Pan Li Hungwei Lin Ye Peng Lipeng Yu Yunyan Zhang Zhongsheng Wang |
| author_sort | Shuang Wang |
| collection | DOAJ |
| description | <i>Sassafras tzumu</i> (Hemsl.) Hemsl., as an Arctic Tertiary relict woody species, is an ecologically and economically important deciduous tree endemic to southern China. Nonetheless, the genetic resources and backgrounds of <i>S. tzumu</i> are still lacking and remain largely unclear. Here, we predicted 16,215 candidate polymorphic nuclear microsatellite (nSSR) loci from the assembled nucleus databases of six geographic-distant individuals of <i>S. tzumu</i> via CandiSSR. Among these nSSRs, the di- (75.53%) and tri-nucleotide (19.75%) repeats were the most abundant, and 27 new polymorphic SSRs were developed and characterized in 136 individuals from six natural populations of <i>S. tzumu</i>. The majority of the above 27 SSRs (24 loci, 88.89%) presented moderate polymorphism (mean <i>PIC</i> = 0.356), and the transferability of these markers in other <i>Sassafras</i> species was high (85.19%). A moderately low level of genetic diversity and a high variation (<i>F</i><sub>ST</sub> = 0.286) of six wild populations of <i>S. tzumu</i> were illuminated by 16 selected polymorphic nSSRs, with the average expected heterozygosity (<i>H</i><sub>E</sub>) of 0.430 at the species level and <i>H</i><sub>E</sub> ranging from 0.195 to 0.387 at the population level. Meanwhile, a bottleneck effect was shown in two populations. Consistent with the results of the principal coordinate analysis (PCoA) and phylogenetic trees, structure analysis optimally divided these six <i>S. tzumu</i> populations into two clusters, and the further strong population subdivision appeared from <i>K</i> = 2 to <i>K</i> = 5, which corresponded to two evolutionarily significant units (ESUs). Moreover, the significant correlation between genetic and geographic distance was tested by the Mantel test (<i>r</i> = 0.742, <i>p</i> = 0.006), clarifying the effect about isolation by distance (IBD), which could be possibly explained by the low gene flow (<i>N</i><sub>m</sub> = 0.625), a relatively high degree of inbreeding (<i>F</i><sub>IS</sub> = 0.166), a relatively large distribution, and mountainous barriers. Above all, our research not only enlarged the useful genetic resources for future studies of population genetics, molecular breeding, and germplasm management of <i>S. tzumu</i> and its siblings but also contributed to proposing scientific conservation strategies and schemes for the better preservation of <i>S. tzumu</i> and other <i>Sassafras</i> (Lauraceae) species. |
| first_indexed | 2024-03-09T19:33:16Z |
| format | Article |
| id | doaj.art-0ed76b401cd34a159be27109e9acd762 |
| institution | Directory Open Access Journal |
| issn | 2223-7747 |
| language | English |
| last_indexed | 2024-03-09T19:33:16Z |
| publishDate | 2022-10-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Plants |
| spelling | doaj.art-0ed76b401cd34a159be27109e9acd7622023-11-24T02:03:55ZengMDPI AGPlants2223-77472022-10-011120270610.3390/plants11202706Genetic Diversity and Population Structure of an Arctic Tertiary Relict Tree Endemic to China (<i>Sassafras tzumu</i>) Revealed by Novel Nuclear Microsatellite (nSSR) MarkersShuang Wang0Ying Wang1Jingbo Zhou2Pan Li3Hungwei Lin4Ye Peng5Lipeng Yu6Yunyan Zhang7Zhongsheng Wang8College of Life Sciences, Nanjing University, Nanjing 210023, ChinaCollege of Life Sciences, Nanjing University, Nanjing 210023, ChinaCollege of Life Sciences, Nanjing University, Nanjing 210023, ChinaSystematic & Evolutionary Botany and Biodiversity Group, MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou 310058, ChinaCollege of Life Sciences, Nanjing University, Nanjing 210023, ChinaCollege of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, ChinaMount Longwang Nature Reserve, Huzhou 313300, ChinaCollege of Life Sciences, Nanjing University, Nanjing 210023, ChinaCollege of Life Sciences, Nanjing University, Nanjing 210023, China<i>Sassafras tzumu</i> (Hemsl.) Hemsl., as an Arctic Tertiary relict woody species, is an ecologically and economically important deciduous tree endemic to southern China. Nonetheless, the genetic resources and backgrounds of <i>S. tzumu</i> are still lacking and remain largely unclear. Here, we predicted 16,215 candidate polymorphic nuclear microsatellite (nSSR) loci from the assembled nucleus databases of six geographic-distant individuals of <i>S. tzumu</i> via CandiSSR. Among these nSSRs, the di- (75.53%) and tri-nucleotide (19.75%) repeats were the most abundant, and 27 new polymorphic SSRs were developed and characterized in 136 individuals from six natural populations of <i>S. tzumu</i>. The majority of the above 27 SSRs (24 loci, 88.89%) presented moderate polymorphism (mean <i>PIC</i> = 0.356), and the transferability of these markers in other <i>Sassafras</i> species was high (85.19%). A moderately low level of genetic diversity and a high variation (<i>F</i><sub>ST</sub> = 0.286) of six wild populations of <i>S. tzumu</i> were illuminated by 16 selected polymorphic nSSRs, with the average expected heterozygosity (<i>H</i><sub>E</sub>) of 0.430 at the species level and <i>H</i><sub>E</sub> ranging from 0.195 to 0.387 at the population level. Meanwhile, a bottleneck effect was shown in two populations. Consistent with the results of the principal coordinate analysis (PCoA) and phylogenetic trees, structure analysis optimally divided these six <i>S. tzumu</i> populations into two clusters, and the further strong population subdivision appeared from <i>K</i> = 2 to <i>K</i> = 5, which corresponded to two evolutionarily significant units (ESUs). Moreover, the significant correlation between genetic and geographic distance was tested by the Mantel test (<i>r</i> = 0.742, <i>p</i> = 0.006), clarifying the effect about isolation by distance (IBD), which could be possibly explained by the low gene flow (<i>N</i><sub>m</sub> = 0.625), a relatively high degree of inbreeding (<i>F</i><sub>IS</sub> = 0.166), a relatively large distribution, and mountainous barriers. Above all, our research not only enlarged the useful genetic resources for future studies of population genetics, molecular breeding, and germplasm management of <i>S. tzumu</i> and its siblings but also contributed to proposing scientific conservation strategies and schemes for the better preservation of <i>S. tzumu</i> and other <i>Sassafras</i> (Lauraceae) species.https://www.mdpi.com/2223-7747/11/20/2706<i>Sassafras tzumu</i>Arctic Tertiary relict plantnuclear microsatellitegenetic diversitypopulation structurepopulation differentiation |
| spellingShingle | Shuang Wang Ying Wang Jingbo Zhou Pan Li Hungwei Lin Ye Peng Lipeng Yu Yunyan Zhang Zhongsheng Wang Genetic Diversity and Population Structure of an Arctic Tertiary Relict Tree Endemic to China (<i>Sassafras tzumu</i>) Revealed by Novel Nuclear Microsatellite (nSSR) Markers Plants <i>Sassafras tzumu</i> Arctic Tertiary relict plant nuclear microsatellite genetic diversity population structure population differentiation |
| title | Genetic Diversity and Population Structure of an Arctic Tertiary Relict Tree Endemic to China (<i>Sassafras tzumu</i>) Revealed by Novel Nuclear Microsatellite (nSSR) Markers |
| title_full | Genetic Diversity and Population Structure of an Arctic Tertiary Relict Tree Endemic to China (<i>Sassafras tzumu</i>) Revealed by Novel Nuclear Microsatellite (nSSR) Markers |
| title_fullStr | Genetic Diversity and Population Structure of an Arctic Tertiary Relict Tree Endemic to China (<i>Sassafras tzumu</i>) Revealed by Novel Nuclear Microsatellite (nSSR) Markers |
| title_full_unstemmed | Genetic Diversity and Population Structure of an Arctic Tertiary Relict Tree Endemic to China (<i>Sassafras tzumu</i>) Revealed by Novel Nuclear Microsatellite (nSSR) Markers |
| title_short | Genetic Diversity and Population Structure of an Arctic Tertiary Relict Tree Endemic to China (<i>Sassafras tzumu</i>) Revealed by Novel Nuclear Microsatellite (nSSR) Markers |
| title_sort | genetic diversity and population structure of an arctic tertiary relict tree endemic to china i sassafras tzumu i revealed by novel nuclear microsatellite nssr markers |
| topic | <i>Sassafras tzumu</i> Arctic Tertiary relict plant nuclear microsatellite genetic diversity population structure population differentiation |
| url | https://www.mdpi.com/2223-7747/11/20/2706 |
| work_keys_str_mv | AT shuangwang geneticdiversityandpopulationstructureofanarctictertiaryrelicttreeendemictochinaisassafrastzumuirevealedbynovelnuclearmicrosatellitenssrmarkers AT yingwang geneticdiversityandpopulationstructureofanarctictertiaryrelicttreeendemictochinaisassafrastzumuirevealedbynovelnuclearmicrosatellitenssrmarkers AT jingbozhou geneticdiversityandpopulationstructureofanarctictertiaryrelicttreeendemictochinaisassafrastzumuirevealedbynovelnuclearmicrosatellitenssrmarkers AT panli geneticdiversityandpopulationstructureofanarctictertiaryrelicttreeendemictochinaisassafrastzumuirevealedbynovelnuclearmicrosatellitenssrmarkers AT hungweilin geneticdiversityandpopulationstructureofanarctictertiaryrelicttreeendemictochinaisassafrastzumuirevealedbynovelnuclearmicrosatellitenssrmarkers AT yepeng geneticdiversityandpopulationstructureofanarctictertiaryrelicttreeendemictochinaisassafrastzumuirevealedbynovelnuclearmicrosatellitenssrmarkers AT lipengyu geneticdiversityandpopulationstructureofanarctictertiaryrelicttreeendemictochinaisassafrastzumuirevealedbynovelnuclearmicrosatellitenssrmarkers AT yunyanzhang geneticdiversityandpopulationstructureofanarctictertiaryrelicttreeendemictochinaisassafrastzumuirevealedbynovelnuclearmicrosatellitenssrmarkers AT zhongshengwang geneticdiversityandpopulationstructureofanarctictertiaryrelicttreeendemictochinaisassafrastzumuirevealedbynovelnuclearmicrosatellitenssrmarkers |