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The Spatial Genetic Structure of Liriodendron chinense Sarg as Revealed by SSR Markers

Author: LiBo
Tutor: LiHuoGen
School: Nanjing Forestry University
Course: Tree Genetics and Breeding
Keywords: Spatial genetic structure Gene flow Pedigree reconstruction Population dynamics Spatial distribution pattern
CLC: S792.21
Type: PhD thesis
Year: 2013
Downloads: 83
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Abstract


Population genetic structure is a major aspect in conservation genetics. It is not only thebasis of the evolution of plants, but also the foundation for the protection of endangered species.Although there are many factors that affect the evolution of plant population, the spatial geneticstructure (SGS) of plants is one of the important factors, for SGS plays key roles in theshort-term evolution. Therefore, studies on SGS may help us to know the population dynamics,as well as to develop effective strategies for ex-situ conservation of endangered species.Liriodendron chinense (Hemsl.) Sarg, a species from the genus of Liriodendron inMagnoliaceae family, is now recognized as an endangered species due to its low ratio of fullseeds, hardness in natural regeneration, small population size and fragmentated habitats. In thispaper, the fine-scale spatical genetic structure of L. chinense was analyzed for three populations(one natural population and two artificial populations) using microsatellite markers. This studyaimed to answer the three following quentions:(1) Is there a strong spatial genetic structurewithin the isolated natural population?(2) Whether the sub-populations grouped by age classcould also exhibit obvious spatial genetic structure?(3) What about the gene flow in the isolatednatural population? In one word, the final goal of this paper is to explore the mechanism of thespatial genetic structure in L. chinense. The main results are as follows:At present, softwares in the basis of maximum likelihood assignment, such as CERVUS,COLONY and PAPA, were often used to analyze parentage. However, the outputs generatedfrom different softwares were much different though applied to the same experimental population.These were mostly attributed to the different characteristics of softwares. In order to compare thepower of three softwares mentioned above on parentage assignment,13microsatellites had beenused to detect an experimental population of Liriodendron which includes278potential parentsand90progenies whose real parents were unknown. Three softwares (CERVUS3.0,COLONY2.0, PAPA2.0) were used to assign parentage for each progeny, the power of threesoftwares were evaluated by checking the assigned parentage to their real parents for eachprogeny. The results are as follows: the average values of number of alleles (A), effective numberof alleles (Ne) and Shannon diversity index (I) in this experimental population were5.23,0.4766,and1.4636respectively, indicating that these13SSR loci were high polymorphic and suitablefor parentage analysis. As a whole, the power of parentage assignment for control pollinationprogenies was higher than that for open pollination progenies, and paternity analysis was betterthan parentage analysis. Each of these three softwares had its specific characteristics. When theywere applied to analyze progenies whose pedigree were not clear, no significant differenceamong three softwares was found when appling to parentage analysis. However, when appling topaternity analysis, the differences among three softwares in terms of power were significant. Theparentage assignment accuracy of CERVUS and COLONY were78.87%and69.90% respectively, much higher than that of PAPA. As for control pollination progeny whose pedigreewas clear, the parentage assignment accuracy of PAPA was34.72%, higher than other twosoftwares when applied to outcrossing progenies. Nevertheless, if applied to selfing progenies,the parentage assignment accuracy of CERVUS and COLONY were83.33%and81.2%respectively, much higher than that of PAPA. Our findings might be helpful in software choicefor parentage analysis in plants.To investigate the spatial genetic structure of Liriodendron chinense, three populations weretaken as target populations, one natural population from Maoershan Reserve, Guilin, Guangxiprovince and two artificial populations from Nanjing and Zhengjiang, Jiangsu provincerespectively.The natural population in Maoershan Reserve is an isolated population and has formedcomplex pedigree relationship in its long-term breeding process. To reconstruct the pedigree ofthis population, all the individuals within this population were detected with17SSR locicombined with chloroplast DNA sequences of PsbA-TrnH gene. Single nucleotide mutation (A/T)among individuals was detected checked. Altogether, there were4types of haplotype in thispopulation. Among49offsprings,47offsprings were successfully assigned to their parentage.The haploid of24offsprings were consistent with their candidate parents.17offsprings coulddistinguish their paternity from maternity. The pedigree of this natural population wasreconstructed based on the results of parentage assignment.The spatial genetic structure for three populations of L.chinense was investigated using17microsatellite markers. The parameters of spatial genetic structure (Sp) of all individuals andtheir offsprings in2artificial populations were0.01341,0.02493and0.01762,0.00989respectively, while in the natural population, the parameters of spatial genetic structure (Sp)were0.02700,0.01423respectively. Alike other species with similar biological characteristics,L.chinense displays strong fine-scale spatial structure in natural population.Gene flow plays key parts in the genetic structure of plant populations. The quantification ofgene flow can be achieved either by parentage analysis directly or by SGS analysis indirectly. Inthis paper, two methods above were used simultaneously to estimate gene flow of L.chinense.The differences among three populations were obvious for both seed flow and pollen flow. Atrend was found that the gene flow and the average pollen dispersal distance decreased withincreased population density in three populations investigated. In two artificial populations withhigher population density, the seed dispersal distance was greater than the pollen dispersaldistance, and the seed flow accounted for the majority of gene flow, while in the naturalpopulation with low population density, the trend was just the opposite.The population structure dynamic of L. chinensis was also analyzed for the naturalpopulation in Maoershan Reserve. Based on the theory of population life table and survivalanalysis, the life table in the natural population of L. chinensis was constructed by replacing ageclasses with size-classes,and the population structure dynamic was also predicted. The censusdata showed that the number of young seedling was larger than that of middle-aged and oldindividuals, indicating that the population was in an incremental status. The survival curve in this population appeared to be a Deevey-Ⅱ type, with a peak of mortality in size class Ⅳ. It can beconcluded that the population size of L. chinensis in Maoer Reserve declined sharply in earlystage,stablized in middle stage and fell rapidly in last stage.The spatial distribution pattern in this natual population of L.chinense was investigated inthe application of O-ring function. The distribution pattern of this population was closely relatedto the spatial scale, with an aggregation distribution in less than24m, a random distribution in24-48m spatial scale, a hypodispersion distribution in49--88m spatial scale and a randomdistribution in larger than88m. The fine-scale spatial distribution pattern was obviousdifferences among growth stages in this natural population. Both the adulted and youngindividuals showed aggregation distribution at smaller spatial scale, and ramdon distribution atother spatial scale. Whereas, for those aging individuals,only one pattern of random distributionwas identified at all spatial scales. The spatial correlation among development stages werepositive at smaller scale,while at larger scale, no close association was identified.The genetic diversity was also compared between parent population and its offspringspopulation based on14SSR loci. Overall, L. chinense contains rather high polymorphismcompared with other species in magnoliaceae. And there was no difference on the geneticdiversity between parent population and offspring population.

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CLC: > Agricultural Sciences > Forestry > Forest tree species > Broad-leaved trees > Liriodendron
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