Genetic diversity and population structure analysis in a large collection of Vicia amoena in China with newly developed SSR markers

AbstractVicia amoena is a high-nutritional quality forage similar to alfalfa. However, studies on the genetic background of V. amoena are scarce. In the present study, the genetic variation of 24 V. amoena populations was assessed with newly developed simple sequence repeat (SSR) markers. A total of 8799 SSRs were identified in the V. amoena genomic-enriched sequences, and the most abundant repeat number was four. A total of 569 sampled individuals were assayed to evaluate the genetic diversity of the V. amoena populations based on 21 polymorphic SSR primers. The polymorphism information content (PIC) ranged from 0.896 to 0.968, with an average of 0.931, which indicated that the markers were highly informative. Based on analysis of molecular variance, 88% of the variance occurred within populations, and the remaining 12% of the variance occurred among populations. The high degree of gene flow (Nm= 4.958) also showed slight differentiation among the V. amoena populations. The V. amoena populations were mainly clustered by steppe and mountain habitats based on principal coordinate analysis (PCoA) and STRUCTURE analysis. This indicated that the elevation and special habitat of geographical origins may be important factors affecting the clustered pattern of V. amoena populations. Neighbour-joining (NJ) analysis did not separate the populations well by geographical origin, which indicated that the genetic structure of V. amoena was complex and needs further study. Overall, our results showed that the newly developed SSR markers could benefit the V. amoena research community by providing genetic background information to help establish a foundation for breeding improvement and germplasm resource conservation.

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Cross Species/Genera Transferability of SSR Markers, Genetic Diversity and Population Structure Analysis in Gladiolus (Gladiolus × grandiflorus L.) Genotypes

10.21203/rs.3.rs-673512/v1 ◽

2021 ◽

Author(s):

Varun Hiremath ◽

Kanwar Pal Singh ◽

Neelu Jain ◽

Kishan Swaroop ◽

Pradeep Kumar Jain ◽

...

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Ssr Markers ◽

Structure Analysis ◽

Genetic Relationships ◽

Crop Improvement ◽

Test Analysis ◽

Average Value ◽

Population Structure Analysis ◽

Genetic Diversity And Structure

Abstract Genetic diversity and structure analysis using molecular markers is necessary for efficient utilization and sustainable management of gladiolus germplasm. Genetic analysis of gladiolus germplasm using SSR markers is largely missing due to scarce genomic information. In the present investigation, we report 66.66% cross transferability of Gladiolus palustris SSRs whereas 48% of Iris EST-SSRs were cross transferable across the gladiolus genotypes used in the study. A total of 17 highly polymorphic SSRs revealed a total 58 polymorphic loci ranging from two to six in each locus with an average of 3.41 alleles per marker. PIC values ranged from 0.11 to 0.71 with an average value of 0.48. Four SSRs were selectively neutral based on Ewens-Watterson test. Analysis of genetic structure of 84 gladiolus genotypes divided whole germplasm into two subpopulations. 35 genotypes were assigned to subpopulation 1 whereas 37 to subpopulation 2 and rest of the genotypes recorded as admixture. Analysis of molecular variance indicated maximum variance (53.59%) among individuals within subpopulations whereas 36.55% of variation observed among individuals within total population. Least variation (9.86%) was noticed between two subpopulations. Moderate (FST = 0.10) genetic differentiation of two subpopulations was observed. Grouping pattern of population structure was consistent with UPGMA dendrogram based on simple matching dissimilarity coefficient (ranged from 01.6 to 0.89) and PCoA. Genetic relationships assessed among the genotypes of respective clusters assist the breeders in selecting desirable parents for crossing. SSR markers from present study can be utilized for cultivar identification, conservation and sustainable utilization of gladiolus genotypes for crop improvement.

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Genetic diversity and population structure analysis of Saccharum and Erianthus genera using microsatellite (SSR) markers

Scientific Reports ◽

10.1038/s41598-018-36630-7 ◽

2019 ◽

Vol 9 (1) ◽

Cited By ~ 8

Author(s):

Ahmad Ali ◽

Yong-Bao Pan ◽

Qin-Nan Wang ◽

Jin-Da Wang ◽

Jun-Lü Chen ◽

...

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Ssr Markers ◽

Structure Analysis ◽

Population Structure Analysis

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Genetic Diversity and Population Structure Analysis of Ever-Bearing and June-Bearing Strawberry Cultivars Using SSR Markers

Korean Journal of Horticultural Science&Technology ◽

10.12972/kjhst.20190030 ◽

2019 ◽

Vol 37 (2) ◽

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Ssr Markers ◽

Structure Analysis ◽

Population Structure Analysis ◽

Strawberry Cultivars

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Genetic Diversity and Population Structure Analysis of Ever-Bearing and June-Bearing Strawberry Cultivars Using SSR Markers

Korean Journal of Horticultural Science&Technology ◽

10.12972/kjhst.20190010 ◽

2019 ◽

Vol 37 (1) ◽

Cited By ~ 1

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Ssr Markers ◽

Structure Analysis ◽

Population Structure Analysis ◽

Strawberry Cultivars

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Genetic Diversity and Population Structure of Traditional Greek and Cypriot Melon Cultigens (Cucumis melo L.) Based on Simple Sequence Repeat Variability

HortScience ◽

10.21273/hortsci.44.7.1820 ◽

2009 ◽

Vol 44 (7) ◽

pp. 1820-1824 ◽

Cited By ~ 13

Author(s):

Emmanouil N. Tzitzikas ◽

Antonio J. Monforte ◽

Abdelhak Fatihi ◽

Zacharias Kypriotakis ◽

Tefkros A. Iacovides ◽

...

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Genetic Variability ◽

Ssr Markers ◽

Structure Analysis ◽

Simple Sequence Repeat ◽

Cucumis Melo ◽

Sequence Repeat ◽

Population Structure Analysis ◽

Simple Sequence

Seventeen simple sequence repeat (SSR) markers were used to assess the genetic diversity and population structure among traditional Greek and Cypriot melon cultigens (Cucumis melo L.). All SSR markers were polymorphic with a total number of 81 alleles, whereas all cultigens could be distinguished with at least one SSR, except cultigens 43 and 41. Reference accessions showed larger genetic variability with an average of four alleles per locus and 0.65 gene of diversity compared with an average of 2.47 alleles per locus and 0.30 of gene diversity for the Greek/Cypriot cultigens. Observed heterozygosity was very low, indicating a lack of outcrossing, at least in recent times. Unrooted neighbor-joining tree analysis and population structure analysis clustered the cultigens and the reference genotypes into five groups. All cultigens could be distinguished; the Cypriot cultigens were more closely related to the inodorus ‘Piel de Sapo’, whereas the Greek cultigens were located in an intermediate position between the inodorus ‘Piel de Sapo’ and the cantalupensis ‘Védrantais’. The cultigen ‘Kokkini’ was the most divergent among the Greek and Cypriot cultigens. This association between geographic origin and genetic similarity among Greek and Cypriot cultigens indicates geographic isolation. Most of the cultivars from the same cultivar group (i.e., inodorus, cantalupensis) clustered together, but some exceptions were found, suggesting that former inodorus landraces would have been transformed to cantalupensis as a result of intercrossing and further selection by farmers. Results of population structure analysis support mixing between cantalupensis and inodorus. ‘Agiou Basileiou’, an inodorus cultigen, was assigned to the subpopulation IV/II of which II is a pure cantalupensis subpopulation. Greek and Cypriot melon cultigens were developed from a broader germplasm base than western Mediterranean cultivars and exhibited useful for melon breeding programs genetic variability.

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Molecular Genetic Diversity and Population Structure Analysis in Chickpea (Cicer arietinum L.) Germplasm using SSR Markers

International Journal of Current Microbiology and Applied Sciences ◽

10.20546/ijcmas.2018.702.079 ◽

2018 ◽

Vol 7 (2) ◽

pp. 639-651 ◽

Cited By ~ 1

Author(s):

S.M. Samyuktha ◽

J.R. Kannan Bapu ◽

S. Geethanjali

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Cicer Arietinum ◽

Ssr Markers ◽

Structure Analysis ◽

Molecular Genetic ◽

Cicer Arietinum L ◽

Molecular Genetic Diversity ◽

Population Structure Analysis

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Genetic Diversity of Paeonia rockii (Flare Tree Peony) Germplasm Accessions Revealed by Phenotypic Traits, EST-SSR Markers and Chloroplast DNA Sequences

Forests ◽

10.3390/f11060672 ◽

2020 ◽

Vol 11 (6) ◽

pp. 672

Author(s):

Xin Guo ◽

Fangyun Cheng ◽

Yuan Zhong

Keyword(s):

Genetic Diversity ◽

Chloroplast Dna ◽

Ssr Markers ◽

Dna Sequences ◽

Genetic Background ◽

Background Information ◽

Phenotypic Traits ◽

Tree Peony ◽

Chloroplast Dna Sequences ◽

Paeonia Rockii

Research Highlights: This study, based on the first collection of cultivated Paeonia rockii (flare tree peony, FTP) germplasm across the main distribution area by our breeding desires, comprehensively evaluates these accessions by using phenotypic traits, expressed sequence tag (EST)-simple sequence repeat (SSR) markers and chloroplast DNA sequences (cpDNA). The results show that these accessions collected selectively by us can represent the genetic background information of FTP as a germplasm of tree crops. Background and Objectives: FTP has high cultural, ornamental and medicinal value traditionally, as well as recently presenting a significance as an emerging edible oil with high α-linolenic acid contents in the seeds. The objectives of this study are to reveal the characteristics of the genetic diversity of FTP, as well as to provide scientific suggestions for the utilization of tree peony breeding and the conservation of germplasm resource. Materials and Methods: Based on the phenotypic traits, EST-SSR markers and chloroplast DNA sequence variation, we studied the diversity of a newly established population of 282 FTP accessions that were collected and propagated by ourselves in our breeding project in recent years. Results: (1) There was an abundant variation in phenotype of the accessions, and the phenotypic variation was evenly distributed within the population, without significant hierarchical structure, (2) the EST-SSR data showed that these 282 accessions had relatively high genetic diversity, in which a total of 185 alleles were detected in 34 pairs of primers. The 282 accessions were divided into three distinct groups, and (3) the chloroplast DNA sequences (cpDNA) data indicated that these accessions had a higher genetic diversity than the population level and a lower genetic diversity than the species level of wild P. rockii, and the existing spatial genetic structure of these accessions can be divided into two branches. Conclusions: From the results of the three analyses, we found that these accessions can fully reflect the genetic background information of FTP germplasm resources, so their protection and utilization will be of great significance for genetic improvement of woody peonies.

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