Genetic Diversity and Population Structure of Potato Germplasm in RDA-Genebank: Utilization for Breeding and Conservation

Potato (Solanum tuberosum L.) is an important staple food and economic crop in many countries. It is of critical importance to understand the genetic diversity and population structure for effective collection, conservation, and utilization of potato germplasm. Thus, the objective of the present study was to investigate the genetic diversity and population structure of potato germplasm conserved in the National Agrobiodiversity Center (NAC) of South Korea to provide basic data for future preservation and breeding of potato genetic resources. A total of 24 simple sequence repeat (SSR) markers were used to assess the genetic diversity and population structure of 482 potato accessions. A total of 257 alleles were detected, with an average of 10.71 alleles per locus. Analysis of molecular variance showed that 97% of allelic diversity was attributed to individual accessions within the population, while only 3% was distributed among populations. Results of genetic structure analysis based on STRUCTURE and discriminant analysis of principal components revealed that 482 potato accessions could be divided into two main subpopulations. Accessions of subpopulation 1 mainly belonged to cultivars and breeding lines. Accessions of subpopulations 2 basically corresponded to wild relatives of potatoes. Results of this study provide useful information for potato improvement and conservation programs, although further studies are needed for a more accurate evaluation of genetic diversity and phenotypic traits of potatoes.

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Analysis of the genetic diversity and population structure of Salix psammophila based on phenotypic traits and simple sequence repeat markers

PeerJ ◽

10.7717/peerj.6419 ◽

2019 ◽

Vol 7 ◽

pp. e6419 ◽

Cited By ~ 2

Author(s):

Lei Hao ◽

Guosheng Zhang ◽

Dongye Lu ◽

Jianjun Hu ◽

Huixia Jia

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Simple Sequence Repeat ◽

Phylogenetic Analyses ◽

Group Method ◽

Phenotypic Traits ◽

Germplasm Management ◽

Sequence Repeat ◽

Marginal Populations ◽

Simple Sequence

Salix psammophila (desert willow) is a shrub endemic to the Kubuqi Desert and the Mu Us Desert, China, that plays an important role in maintaining local ecosystems and can be used as a biomass feedstock for biofuels and bioenergy. However, the lack of information on phenotypic traits and molecular markers for this species limits the study of genetic diversity and population structure. In this study, nine phenotypic traits were analyzed to assess the morphological diversity and variation. The mean coefficient of variation of 17 populations ranged from 18.35% (branch angle (BA)) to 38.52% (leaf area (LA)). Unweighted pair-group method with arithmetic mean analysis of nine phenotypic traits of S. psammophila showed the same results, with the 17 populations clustering into five groups. We selected 491 genets of the 17 populations to analyze genetic diversity and population structure based on simple sequence repeat (SSR) markers. Analysis of molecular variance (AMOVA) revealed that most of the genetic variance (95%) was within populations, whereas only a small portion (5%) was among populations. Moreover, using the animal model with SSR-based relatedness estimated of S. psammophila, we found relatively moderate heritability values for phenotypic traits, suggesting that most of trait variation were caused by environmental or developmental variation. Principal coordinate and phylogenetic analyses based on SSR data revealed that populations P1, P2, P9, P16, and P17 were separated from the others. The results showed that the marginal populations located in the northeastern and southwestern had lower genetic diversity, which may be related to the direction of wind. These results provide a theoretical basis for germplasm management and genetic improvement of desert willow.

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Molecular Genetic Diversity and Population Structure of Ginseng Germplasm in RDA-Genebank: Implications for Breeding and Conservation

Agronomy ◽

10.3390/agronomy10010068 ◽

2020 ◽

Vol 10 (1) ◽

pp. 68 ◽

Cited By ~ 2

Author(s):

Kyung Jun Lee ◽

Jung-Ro Lee ◽

Raveendar Sebastin ◽

Gyu-Taek Cho ◽

Do Yoon Hyun

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Ssr Markers ◽

Gene Diversity ◽

Research Effort ◽

Molecular Genetic ◽

Allelic Diversity ◽

Perennial Herb ◽

Molecular Evidence ◽

Breeding Lines

Ginseng (Panax ginseng C.A. Meyer), commonly known as Korean or Asian ginseng, is a perennial herb native to Korea and China. There has been limited research effort to analyze the genetic diversity and population structure of ginseng germplasm because of its growth habits. In the present study, genetic diversity and population structure of ginseng germplasm conserved in the National Agrobiodiversity Center (NAC) of South Korea were analyzed to provide basic data for future preservation and breeding of ginseng genetic resources. Seventeen simple sequence repeat (SSR) markers were used to assess the genetic diversity and population structure of 1109 ginseng accessions. Among 1109 ginseng accessions, 1042 (94.0%) accessions were landraces and 66 (6.0%) accessions were breeding lines (61 accessions, 5.5%) or cultivars (5 accessions, 0.5%). SSR markers revealed 56 different alleles with an average of 3.29 alleles per locus. The average gene diversity was 0.49. Analysis of molecular variance showed that 91% of allelic diversity was attributed to individual accessions within clusters while only 9% was distributed among clusters. Using discriminant analysis of principal components, 12 clusters were detected in 1109 ginseng accessions. The results of this study provide molecular evidence for the narrow genetic base of ginseng germplasm in NAC. For the broad understanding and efficient use of ginseng germplasm, it is necessary to analyze functional factors and to evaluate morphological traits.

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

10.1101/2020.08.12.247718 ◽

2020 ◽

Author(s):

Liu Shuo ◽

Decroocq Stephane ◽

Harte Elodie ◽

Tricon David ◽

Chague Aurelie ◽

...

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Core Collection ◽

Genetic Relationships ◽

Allelic Diversity ◽

Wild Relatives ◽

Ex Situ ◽

Conservation Measures ◽

Geographical Regions

AbstractIn-depth characterization of the genetic diversity and population structure of wild relatives of crops is of paramount importance for genetic improvement and biodiversity conservation, and is particularly crucial when the wild relatives of crops are endangered. In this study, we therefore sampled the Alpine plum (Briançon apricot) Prunus brigantina Vill. across its natural distribution in the French Alps, where its populations are severely fragmented and its population size strongly impacted by humans. We analysed 71 wild P. brigantina samples with 34 nuclear markers and studied their genetic diversity and population structure, with the aim to inform in situ conservation measures and build a core collection for long-term ex-situ conservation. We also examined the genetic relationships of P. brigantina with other species in the Prunophora subgenus, encompassing the Prunus (Eurasian plums), Prunocerasus (North-American plums) and Armeniaca (apricots) sections, to check its current taxonomy. We detected a moderate genetic diversity in P. brigantina and a Bayesian model-based clustering approach revealed the existence of three genetically differentiated clusters, endemic to three geographical regions in the Alps, which will be important for in situ conservation measures. Based on genetic diversity and population structure analyses, a subset of 36 accessions were selected for ex-situ conservation in a core collection that encompasses the whole detected P. brigantina allelic diversity. Using a dataset of cultivated apricots and wild cherry plums (P. cerasifera) genotyped with the same markers, we detected gene flow neither with European P. armeniaca cultivars nor with diploid plums. In contrast with previous studies, dendrograms and networks placed P. brigantina closer to Armeniaca species than to Prunus species. Our results thus confirm the classification of P. brigantina within the Armeniaca section; it also illustrates the importance of the sampling size and design in phylogenetic studies.

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Genetic diversity in three groups of barley germplasm assessed by simple sequence repeats

Genome ◽

10.1139/g02-071 ◽

2002 ◽

Vol 45 (6) ◽

pp. 1095-1106 ◽

Cited By ~ 111

Author(s):

I A Matus ◽

P M Hayes

Keyword(s):

Genetic Diversity ◽

Hordeum Vulgare ◽

Molecular Marker ◽

Mapping Population ◽

Allelic Diversity ◽

Breeding Lines ◽

Barley Germplasm ◽

High Level ◽

Elite Breeding Lines ◽

Simple Sequence

Genetic diversity can be measured by several criteria, including phenotype, pedigree, allelic diversity at marker loci, and allelic diversity at loci controlling phenotypes of interest. Abundance, high level of polymorphism, and ease of genotyping make simple sequence repeats (SSRs) an excellent molecular marker system for genetics diversity analyses. In this study, we used a set of mapped SSRs to survey three representative groups of barley germplasm: a sample of crop progenitor (Hordeum vulgare subsp. spontaneum) accessions, a group of mapping population parents, and a group of varieties and elite breeding lines. The objectives were to determine (i) how informative SSRs are in these three sets of barley germplasm resources and (ii) the utility of SSRs in classifying barley germplasm. A total of 687 alleles were identified at 42 SSR loci in 147 genotypes. The number of alleles per locus ranged from 4 to 31, with an average of 16.3. Crop progenitors averaged 10.3 alleles per SSR locus, mapping population parents 8.3 alleles per SSR locus, and elite breeding lines 5.8 alleles per SSR locus. There were many exclusive (unique) alleles. The polymorphism information content values for the SSRs ranged from 0.08 to 0.94. The cluster analysis indicates a high level of diversity within the crop progenitors accessions and within the mapping population parents. It also shows a lower level of diversity within the elite breeding germplasm. Our results demonstrate that this set of SSRs was highly informative and was useful in generating a meaningful classification of the germplasm that we sampled. Our long-term goal is to determine the utility of molecular marker diversity as a tool for gene discovery and efficient use of germplasm.Key words: Hordeum vulgare subsp. vulgare, Hordeum vulgare subsp. spontaneum, SSR, genetic diversity, germplasm.

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