Molecular genetic diversity and population structure of a selected core set in garlic and its relatives using novel SSR markers

Chickpea (Cicer arietinum L.) is a cheap source of protein and rich in minerals for people living in developing countries. In order to assess the existing molecular genetic diversity and determine population structures in selected Ethiopian chickpea germplasm accessions (118), a set of 46 simple sequence repeat (SSR) markers equally distributed on the chickpea genome were genotyped. A total of 572 alleles were detected from 46 SSR markers, and the number of alleles per locus varied from 2 (ICCM0289) to 28 (TA22). The average number of alleles per locus, polymorphism information content, and expected heterozygosity were 12, 0.684, and 0.699, respectively. Phylogenetic analysis grouped the 118 chickpea genotypes from diverse sources into three evolutionary and/or biological groups (improved desi, improved kabuli, and landraces). The population structure analysis revealed six sub-populations from 118 chickpea genotypes studied. AMOVA revealed that 57%, 29%, and 14% of the total genetic variations were observed among individuals, within populations, and among populations. The insights into the genetic diversity at molecular levels in the Ethiopian germplasm lines can be used for designing conservation strategies as well as the diverse germplasm lines identified in this study can be used for trait dissection and trait improvement.

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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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Molecular genetic diversity and population structure of Ethiopian white lupin landraces: Implications for breeding and conservation

PLoS ONE ◽

10.1371/journal.pone.0188696 ◽

2017 ◽

Vol 12 (11) ◽

pp. e0188696 ◽

Cited By ~ 8

Author(s):

Mulugeta Atnaf ◽

Nasser Yao ◽

Kyalo Martina ◽

Kifle Dagne ◽

Dagne Wegary ◽

...

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Molecular Genetic ◽

White Lupin ◽

Molecular Genetic Diversity

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Molecular genetic diversity and population structure in Eucalyptus pauciflora subsp. pauciflora (Myrtaceae) on the island of Tasmania

Australian Journal of Botany ◽

10.1071/bt14036 ◽

2014 ◽

Vol 62 (3) ◽

pp. 175 ◽

Cited By ~ 12

Author(s):

Archana Gauli ◽

Dorothy A. Steane ◽

René E. Vaillancourt ◽

Brad M. Potts

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Molecular Genetic ◽

Glacial Refugia ◽

Altitudinal Distribution ◽

The North ◽

Chloroplast Haplotype ◽

Molecular Genetic Diversity ◽

Nuclear Microsatellite ◽

Chloroplast Dna Markers

Genetic diversity and population structure of Tasmanian populations of Eucalyptus pauciflora were assessed using chloroplast and nuclear microsatellite markers. Maternal trees and open-pollinated progeny from 37 populations were sampled across the species’ geographic and altitudinal distribution in Tasmania. The distribution of chloroplast haplotype richness showed a clear geographic structure with suggestion of three major refugia (Storm Bay, Tamar Valley and St Pauls River Valley), two of which are consistent with previously reported glacial refugia. Chloroplast haplotype affinities provided evidence of migration of populations from the north and east towards the south and west of Tasmania. High nuclear microsatellite diversity was observed across the species’ range. Most of this variation was distributed within populations with low but significant FST, suggesting high gene flow among populations that is more pronounced in mature stands. Higher nuclear genetic diversity in newly colonised areas compared with lowland putative refugial regions, and the converse in chloroplast DNA markers, suggest limited seed dispersal into newly colonised regions combined with high pollen flow between different source populations in newly colonised areas. Our results do not support the suggestion that highland populations of E. pauciflora originate from in situ high-altitude refugia, but instead argue they originate from lowland refugia.

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Genetic diversity and SSR markers development of ancient Camellia sinensis in Sandu County of Guizhou Province

10.21203/rs.3.rs-208220/v1 ◽

2021 ◽

Author(s):

Yichen Zhao ◽

Runying Wang ◽

Qing Liu ◽

Xuan Dong ◽

De-Gang Zhao

Keyword(s):

Genetic Diversity ◽

Ssr Markers ◽

Diversity Index ◽

Molecular Genetic ◽

Diversity Indices ◽

Guizhou Province ◽

Information Index ◽

Molecular Genetic Diversity ◽

Qualitative Characters ◽

Breed Selection

Abstract Background: The genetic abundance of ancient tea germplasm has been preserved in the long evolution process, which provides valuable resources for the protection and breed selection of ancient tea germplasm. However, the limited studies related to the genetic diversity of ancient tea germplasm restrict protection and breed selection. Therefore, the genetic diversity of ancient tea germplasm in Sandu county of Guizhou Province was explored in this study. II.Methods and Results: The genetic diversity was analyzed using phenotypes and SSR markers. The ranges for the variation coefficients of the six quantitative and seven qualitative characters were 17.76%-60.37% and 18.58%-50.64%, respectively. The ranges of diversity indices of the six quantitative and seven qualitative characters were 1.72-2.74 and 0.55-0.84, respectively. Ninety-six bands were amplified using 15 pairs of SSR primers from the 145 samples, and the average polymorphism information index was 0.66. The analysis revealed that the average values of Nei’s genetic diversity index (H) and the Shannon information index (I) are 0.26 and 0.41, respectively. Further, a genetic similarity coefficient of 0.734 shown by UPGMA dendrogram classified the 145 samples decreased into four groups. III.Conclusions: This study revealed the rich phenotypic variation and high molecular genetic diversity and the genetic diversity of the arbor is higher than that of the shrub of the ancient tea germplasm in Sandu of Guizhou province. Thus, this study not only provides a theoretical basis for the protection and breed selection but also promotes further research of ancient tea germplasm.

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Genetic Diversity and Population Structure of Faba Bean (Vicia faba) from Turkey

HortScience ◽

10.21273/hortsci11022-16 ◽

2016 ◽

Vol 51 (8) ◽

pp. 980-983

Author(s):

Şurhan Göl ◽

Sami Doğanlar ◽

Anne Frary

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Vicia Faba ◽

Ssr Markers ◽

Faba Bean ◽

High Efficiency ◽

Starch Content ◽

Molecular Genetic ◽

Distance Matrix ◽

High Genetic Diversity

Faba bean (Vicia faba L.) is an important food and feed legume because of the nutritional value of its seed protein and starch content, good biomass, and high efficiency nitrogen fixation. This study analyzed the molecular genetic diversity and population structure of 101 Turkish faba bean accessions using simple sequence repeat (SSR) markers. A total of 32 SSR markers yielded 281 loci of which 277 (98.6%) were polymorphic. Mean dissimilarity between genotypes was 0.355, a relatively high value which was expected given faba bean’s large genome and limited breeding history. According to the results, faba bean individuals grouped into three main clusters based on both distance matrix (neighbor-joining algorithm) and model-based (population structure) clustering analyses. Clustering was not correlated with seed size or origin within Turkey. Six cultivars were included in the analysis and showed high genetic diversity compared with the landraces, as expected, given the fact that at least some of the cultivars were bred by hybridization. A total of 47 individuals were selected for the core collection to represent the diversity of Turkish faba bean germplasm. This core set encompasses material adapted to all growing regions and should be a priority for morphological characterization.

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