Genetic diversity and population structure analyses in the Alpine plum (Prunus brigantina Vill.) confirm its affiliation to the Armeniaca section

Liu, Shuo; Decroocq, Stéphane; Harte, Elodie; Torgerson, David; Chague, Aurélie; Balakishiyeva, Gulnara; Kostritsyna, Tatiana; Turdiev, Timur; Saux, M. Fisher-Le; Dallot, Sylvie; Giraud, Tatiana; Decroocq, Véronique

doi:10.1007/s11295-020-01484-6

Cited by 10 publications

(17 citation statements)

References 41 publications

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“…Here, the core set was used to detect novel variations, select superior varieties, and furnish optimal germplasms because it consists of relatively smaller populations with comparatively higher genetic diversity [ 62 ]. Core collection development has been applied for cowpea [ 63 ], alpine plum [ 64 ], walnut [ 65 ], tea [ 50 , 57 ] and other plants. However, no core collection has yet been developed for the cultivated-type tea accessions in Guizhou Plateau.…”

Section: Discussionmentioning

confidence: 99%

Population structure analysis to explore genetic diversity and geographical distribution characteristics of cultivated-type tea plant in Guizhou Plateau

et al. 2022

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Background Tea plants originated in southwestern China. Guizhou Plateau is an original center of tea plants, and is rich in germplasm resources. However, the genetic diversity, population structure and distribution characteristics of cultivated-type tea plants in the region are unknown. In this study, we explored the genetic diversity and geographical distribution of cultivated-type tea accessions in Guizhou Plateau. Results We used 112,072 high-quality genotyping-by-sequencing to analyze the genetic diversity, principal components, phylogeny, population structure, and linkage disequilibrium, and develop a core collection of 253 cultivated-type tea plant accessions from Guizhou Plateau. The results showed Genetic diversity of the cultivated-type tea accessions of the Pearl River Basin was significantly higher than that of the cultivated-type tea accessions of the Yangtze River Basin. Three inferred pure groups (CG-1, CG-2 and CG-3) and one inferred admixture group (CG-4), were identified by a population structure analysis, and verified by principal component and phylogenetic analyses. The highest genetic distance and differentiation coefficients were determined for CG-2 vs CG-3. The lower genetic distance and differentiation coefficients were determined for CG-4 vs CG-2 and CG-4 vs CG-3, respectively. We developed a core set and a primary set. The primary and core sets contained 77.0 and 33.6% of all individuals in the initial set, respectively. The primary set may serve as the primary population in genome-wide association studies, while the core collection may serve as the core population in multiple treatment setting studies. Conclusions The present study demonstrated the genetic diversity and geographical distribution characteristics of cultivated-type tea plants in Guizhou Plateau. Significant differences in genetic diversity and evolutionary direction were detected between the ancient landraces of the Pearl River Basin and the those of the Yangtze River Basin. Major rivers and ancient hubs were largely responsible for the genetic exchange between the Pearl River Basin and the Yangtze River Basin ancient landraces as well as the formation of the ancient hubs evolutionary group. Genetic diversity, population structure and core collection elucidated by this study will facilitate further genetic studies, germplasm protection, and breeding of tea plants.

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Section: Discussionmentioning

confidence: 99%

Population structure analysis to explore genetic diversity and geographical distribution characteristics of cultivated-type tea plant in Guizhou Plateau

et al. 2022

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“…Mountains and rivers function as natural geographical barriers affecting gene ow in plants [6][7][8]. Moreover, human disturbances, such as road or bridge construction and mining, can signi cantly increase geographical isolation and habitat fragmentation of populations, resulting in reduced gene ow and genetic diversity of populations, thus affecting the genetic structure and population dynamics of the species [9][10][11][12]. Even forest park tourism and farming, which have recently become popular in China, pose a threat to rare species.…”

Section: Introductionmentioning

confidence: 99%

Genetic diversity, population genetic structure and gene flow in the rare and endangered wild plant Cypripedium macranthos revealed by genotyping-by-sequencing

Wu¹,

Dong

Zhao³

et al. 2022

Preprint

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Background: Genetic diversity, genetic structure, and gene flow in plant populations and their influencing factors are important in conservation biology. Cypripedium macranthos isone of the few wild orchids with high ornamental value in northern China. However, over the past decade, excessive collection, trading, tourism development, habitat fragmentation, deceptive pollination, and seed germination difficulties have all caused a sharp decline in the number of C. macranthos individuals and its population. In order to propose a scientific and effective conservation strategy, the genetic diversity, genetic structure and gene flow of the current CM population are urgent scientific issues to be clarified. Results: Here, 99 individuals of C. macranthos from north and northeastChina were analyzed to evaluate the genetic diversity, gene flow among populations, and genetic structure by genotyping-by-sequencing. More than 68.44 Gbhigh-quality clean reads and 41,154 SNPs were obtained. Our data based on bioinformatics methods revealed that C. macranthos has lower genetic diversity, high levels of historical gene flow, and moderate-to-high genetic differentiation between populations. The gene migration model revealed that the direction of gene flow was mainly from northeast populations to north populations in China. The results of genetic structure analysis showed that 11 C. macranthos populations can be considered as two groups, and further divided into four subgroups. Moreover, the Mantel test detected no significant “Isolation by Distance” between populations. Conclusions: Our study demonstrates that the present genetic diversity andgenetic structure of C. macranthos populations weremainly caused by biological characteristics, human interference, habitat fragmentation, and restricted gene flow. Finally, constructive measures, which can provide a basis for the proposal of conservation strategies, have been suggested.

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“…ansu population revealed high levels of genetic diversity (He = 0.696). This level of diversity was higher than that of Prunus mume (He = 0.497) [ 47 ], and Prunus brigantina (He = 0.48) [ 48 ], but lower than that of Prunus sibirica (He = 0.774) [ 21 ] and Prunus armeniaca (He = 0.792) [ 13 ]. The level of genetic diversity may be related to molecular markers, samples, environmental conditions, and other factors.…”

Section: Discussionmentioning

confidence: 99%

Genetic diversity of Prunus armeniaca L. var. ansu Maxim. germplasm revealed by simple sequence repeat (SSR) markers

Chen

Liu²,

Lu³

et al. 2022

PLoS ONE

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The genetic diversity and genetic structure of P. armeniaca var. ansu were analyzed based on SSR markers. The aim was to provide scientific basis for conservation, efficient utilization, molecular marker assisted breeding and improved variety selection of P. armeniaca var. ansu germplasm resources. The results showed that the level of genetic diversity within the population was high. Among the 30 SSR markers, the mean number of observed alleles was 11.433, the mean number of effective alleles was 4.433, the mean of Shannon information index was 1.670, and the mean of polymorphic information content was 0.670. Among the eight provenances, Tuanjie Township, Xinyuan County, Xinjiang had the highest genetic diversity. The observed alleles, effective alleles, Shannon information index and Nei’s gene diversity index among provenances were higher than those within provenances. Based on Bayesian mathematical modeling and UPGMA cluster analysis, 86 P. armeniaca var. ansu accessions were divided into three subpopulations and four groups, which reflected individual differences in provenances. Subpopulations classified by Bayesian mathematical modeling and groups classified by UPGMA cluster analysis were significantly correlated with geographical provenance (Sig<0.01) and the provenances significantly impacted classification of groups. The provenances played an important role in classification of groups. The genetic distance between Tuanjie Township of Xinyuan County and Alemale Township of Xinyuan County was the smallest, while the genetic relationship between them was the closest and the degree of genetic differentiation was small.

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Genetic diversity and population structure analyses in the Alpine plum (Prunus brigantina Vill.) confirm its affiliation to the Armeniaca section

Cited by 10 publications

References 41 publications

Population structure analysis to explore genetic diversity and geographical distribution characteristics of cultivated-type tea plant in Guizhou Plateau

Population structure analysis to explore genetic diversity and geographical distribution characteristics of cultivated-type tea plant in Guizhou Plateau

Genetic diversity, population genetic structure and gene flow in the rare and endangered wild plant Cypripedium macranthos revealed by genotyping-by-sequencing

Genetic diversity of Prunus armeniaca L. var. ansu Maxim. germplasm revealed by simple sequence repeat (SSR) markers

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