Genetic diversity analysis and the genetic fingerprinting of 33 DUS test standard tobacco varieties

Abstract Background: At present, the distinctness, uniformity, and stability (DUS) testing of flue-cured tobacco ( Nicotiana tabacum L.) depends on field morphological identification, which is problematic in that it is intensive, time-consuming, and susceptible to environmental impacts. In order to improve the efficiency and accuracy of tobacco DUS testing, the development of a molecular marker-based method for genetic diversity identification is urgently needed. Results: In total, 91 simple sequence repeats (SSR) markers with clear and polymorphic amplification bands were obtained with polymorphism information content, Nei index, and Shannon information index values of 0.3603, 0.4040, and 0.7228, respectively. Clustering analysis showed that the 33 study varieties, which are standard varieties for flue-cured tobacco DUS testing, could all be distinguished from one another. Further analysis showed that a minimum of 25 markers were required to identify the genetic diversity of these varieties. Following the principle of two markers per linkage group, 48 pairs of SSR markers were selected. Correlation analysis showed that the genetic relationships revealed by the 48 SSR markers were consistent with those found using the 91 SSR markers. Conclusions: The genetic fingerprints of the 33 standard varieties of flue-cured tobacco were constructed using 48 SSR markers, and an SSR marker-based identification technique for new tobacco varieties was developed. This study provides a reliable technological approach for determining the novelty of new tobacco varieties and offers a solid technical basis for the accreditation and protection of new tobacco varieties.

Download Full-text

Genetic diversity and fingerprinting of 33 standard flue-cured tobacco varieties for use in distinctness, uniformity, and stability testing

10.21203/rs.2.20461/v3 ◽

2020 ◽

Author(s):

Binbin He ◽

Ruimei Geng ◽

Lirui Cheng ◽

Xianbin Yang ◽

Hongmei Ge ◽

...

Keyword(s):

Genetic Diversity ◽

Ssr Markers ◽

Genetic Relationships ◽

Morphological Identification ◽

Information Index ◽

Nicotiana Tabacum L ◽

Dus Testing ◽

Identification Technique ◽

Technical Basis ◽

Simple Sequence

Abstract Background: At present, the distinctness, uniformity, and stability (DUS) testing of flue-cured tobacco ( Nicotiana tabacum L.) depends on field morphological identification, which is problematic in that it is intensive, time-consuming, and susceptible to environmental impacts. In order to improve the efficiency and accuracy of tobacco DUS testing, the development of a molecular marker-based method for genetic diversity identification is urgently needed. Results: In total, 91 simple sequence repeats (SSR) markers with clear and polymorphic amplification bands were obtained with polymorphism information content, Nei index, and Shannon information index values of 0.3603, 0.4040, and 0.7228, respectively. Clustering analysis showed that the 33 study varieties, which are standard varieties for flue-cured tobacco DUS testing, could all be distinguished from one another. Further analysis showed that a minimum of 25 markers were required to identify the genetic diversity of these varieties. Following the principle of two markers per linkage group, 48 pairs of SSR markers were selected. Correlation analysis showed that the genetic relationships revealed by the 48 SSR markers were consistent with those found using the 91 SSR markers. Conclusions: The genetic fingerprints of the 33 standard varieties of flue-cured tobacco were constructed using 48 SSR markers, and an SSR marker-based identification technique for new tobacco varieties was developed. This study provides a reliable technological approach for determining the novelty of new tobacco varieties and offers a solid technical basis for the accreditation and protection of new tobacco varieties.

Download Full-text

Genetic diversity and fingerprinting of 33 standard flue-cured tobacco varieties for use in distinctness, uniformity, and stability testing

10.21203/rs.2.20461/v2 ◽

2020 ◽

Author(s):

Binbin He ◽

Ruimei Geng ◽

Lirui Cheng ◽

Xianbin Yang ◽

Hongmei Ge ◽

...

Keyword(s):

Genetic Diversity ◽

Ssr Markers ◽

Genetic Relationships ◽

Morphological Identification ◽

Information Index ◽

Nicotiana Tabacum L ◽

Dus Testing ◽

Identification Technique ◽

Technical Basis ◽

Simple Sequence

Abstract Background: At present, the distinctness, uniformity, and stability (DUS) testing of flue-cured tobacco ( Nicotiana tabacum L.) depends on field morphological identification, which is problematic in that it is intensive, time-consuming, and susceptible to environmental impacts. In order to improve the efficiency and accuracy of tobacco DUS testing, the development of a molecular marker-based method for genetic diversity identification is urgently needed. Results: In total, 91 simple sequence repeats (SSR) markers with clear and polymorphic amplification bands were obtained with polymorphism information content, Nei index, and Shannon information index values of 0.3603, 0.4040, and 0.7228, respectively. Clustering analysis showed that the 33 study varieties, which are standard varieties for flue-cured tobacco DUS testing, could all be distinguished from one another. Further analysis showed that a minimum of 25 markers were required to identify the genetic diversity of these varieties. Following the principle of two markers per linkage group, 48 pairs of SSR markers were selected. Correlation analysis showed that the genetic relationships revealed by the 48 SSR markers were consistent with those found using the 91 SSR markers. Conclusions: The genetic fingerprints of the 33 standard varieties of flue-cured tobacco were constructed using 48 SSR markers, and an SSR marker-based identification technique for new tobacco varieties was developed. This study provides a reliable technological approach for determining the novelty of new tobacco varieties and offers a solid technical basis for the accreditation and protection of new tobacco varieties.

Download Full-text

Genetic diversity among silkworm (Bombyx mori L., Lep., Bombycidae) germplasms revealed by microsatellites

Genome ◽

10.1139/g05-053 ◽

2005 ◽

Vol 48 (5) ◽

pp. 802-810 ◽

Cited By ~ 30

Author(s):

Muwang Li ◽

Li Shen ◽

Anying Xu ◽

Xuexia Miao ◽

Chengxiang Hou ◽

...

Keyword(s):

Genetic Diversity ◽

Bombyx Mori ◽

Ssr Markers ◽

Simple Sequence Repeat ◽

Genetic Relationships ◽

Group Method ◽

Sequence Repeat ◽

Bombyx Mori L ◽

Simple Sequence ◽

Silkworm Bombyx Mori

To determine genetic relationships among strains of silkworm, Bombyx mori L., 31 strains with different origins, number of generations per year, number of molts per generation, and morphological characters were studied using simple sequence repeat (SSR) markers. Twenty-six primer pairs flanking microsatellite sequences in the silkworm genome were assayed. All were polymorphic and unambiguously separated silkworm strains from each other. A total of 188 alleles were detected with a mean value of 7.2 alleles/locus (range 2–17). The average heterozygosity value for each SSR locus ranged from 0 to 0.60, and the highest one was 0.96 (Fl0516 in 4013). The mean polymorphism index content (PIC) was 0.66 (range 0.12–0.89). Unweighted pair group method with arithmetic means (UPGMA) cluster analysis of Nei's genetic distance grouped silkworm strains based on their origin. Seven major ecotypic silkworm groups were analyzed. Principal components analysis (PCA) for SSR data support their UPGMA clustering. The results indicated that SSR markers are an efficient tool for fingerprinting cultivars and conducting genetic-diversity studies in the silkworm.Key words: silkworm, Bombyx mori L., microsatellites, simple sequence repeat (SSR), genetic diversity.

Download Full-text

Genetic diversity analysis of yam cultivars (Dioscorea rotundata Poir.) in Benin using simple sequence repeat (SSR) markers

Plant Genetic Resources ◽

10.1017/s1479262107672323 ◽

2007 ◽

Vol 5 (02) ◽

pp. 71-81 ◽

Cited By ~ 23

Author(s):

Serge Tostain ◽

Clément Agbangla ◽

Nora Scarcelli ◽

Cédric Mariac ◽

Ogoubi Daïnou ◽

...

Keyword(s):

Genetic Diversity ◽

Ssr Markers ◽

Simple Sequence Repeat ◽

Management Practices ◽

Genetic Relationships ◽

Sequence Repeat ◽

Dioscorea Rotundata ◽

Tuber Crop ◽

The Mean ◽

Simple Sequence

Guinea yam (Dioscorea rotundataPoir.) is a dioecious vegetatively propagated tuber crop. It is widely cultivated by traditional techniques in West Africa, its area of origin. The genetic diversity of 146 accessions from Benin was analysed using 10 polymorphic simple sequence repeat (SSR) nuclear markers and agromorphological traits. An average of 8.4 alleles per locus was detected. The mean heterozygosity was 0.57 and the mean polymorphism information content (PIC) for polymorphic markers was 0.51. Some cultivars (23%) were found to have an identical genotype for the 10 markers. The structure of the genetic diversity observed in Benin is the result of farmers' crop management practices and their know-how. The cultivar diversity had a geographical component. We also noted major differentiation between early and late cultivars, with higher diversity in the early ones. Cultivars from northern Benin and early cultivars had the greatest allelic richness. SSR markers proved to be powerful tools for fingerprinting each cultivar and analysing their genetic relationships. The results of this study could be useful for defining a strategy for the conservation of genetic diversity in yams.

Download Full-text

SSR molecular marker analysis of the grapevine germplasm of Montenegro

OENO One ◽

10.20870/oeno-one.2014.48.2.1562 ◽

2014 ◽

Vol 48 (2) ◽

pp. 87 ◽

Cited By ~ 2

Author(s):

Vesna Maraš ◽

Vladan Bozovic ◽

Sabrina Giannetto ◽

Manna Crespan

Keyword(s):

Molecular Marker ◽

Detailed Analysis ◽

Ssr Markers ◽

Simple Sequence Repeat ◽

Genetic Relationships ◽

Morphological Variability ◽

Sequence Repeat ◽

Molecular Databases ◽

Molecular Marker Analysis ◽

Simple Sequence

Aim: Given that the information about the origin, genetic relationships, and diversity of Montenegrin grapevines is still partial, we performed a detailed analysis of the germplasm in this country using simple sequence repeat (SSR) markers. Our main goal was to determine the identity of cultivars unique to Montenegro and those shared with other countries, especially the neighbouring ones.Methods and results: Seventy samples were collected and 14 genotypes were found. After SSR profile comparison with available molecular databases and literature data, the identity of each genotype was established. Five well-known cultivars were found, the others being minor, lesser-known cultivars.Conclusion: This research provides an overview of the Montenegrin grapevine assortment. There are cultivars shared with other countries, mainly the neighbouring ones, while others are likely native to Montenegro. The Kratošija population (alias Primitivo, Zinfandel and Crljenak Kaštelanski) has a large number of different names in Montenegro and also a wide morphological variability. Therefore, Montenegro is the best candidate as the origin and spreading point of this cultivar.Significance and impact of the study: The present study adds information on the identity, origin, diffusion and variability of some grapevine cultivars, allowing us to reconstruct the history and evolution of national and transnational ampelographic assortment of Montenegro.

Download Full-text

Mining and validation of novel genotyping-by-sequencing (GBS)-based simple sequence repeats (SSRs) and their application for the estimation of the genetic diversity and population structure of coconuts (Cocos nucifera L.) in Thailand

Horticulture Research ◽

10.1038/s41438-020-00374-1 ◽

2020 ◽

Vol 7 (1) ◽

Author(s):

Kanamon Riangwong ◽

Samart Wanchana ◽

Wanchana Aesomnuk ◽

Chatree Saensuk ◽

Phakchana Nubankoh ◽

...

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Ssr Markers ◽

Molecular Breeding ◽

Reference Genome ◽

Genetic Relationships ◽

Cocos Nucifera ◽

Genotyping By Sequencing ◽

Phylogenetic Tree Analysis ◽

Simple Sequence

Abstract Coconut (Cocos nucifera L.) is an important economic crop in tropical countries. However, the lack of a complete reference genome and the limitations of usable DNA markers hinder genomic studies and the molecular breeding of coconut. Here, we present the results of simple sequence repeat (SSR) mining from a high-throughput genotyping-by-sequencing (GBS) study of a collection of 38 coconut accessions. A total of 22,748 SSRs with di-, tri-, tetra-, penta- and hexanucleotide repeats of five or more were identified, 2451 of which were defined as polymorphic loci based on locus clustering in 38 coconut accessions, and 315 loci were suitable for the development of SSR markers. One hundred loci were selected, and primer pairs for each SSR locus were designed and validated in 40 coconut accessions. The analysis of 74 polymorphic markers identified between 2 and 9 alleles per locus, with an average of 3.01 alleles. The assessment of the genetic diversity and genetic relationships among the 40 coconut varieties based on the analysis of population structure, principal coordinate analysis (PCoA), and phylogenetic tree analysis using the 74 polymorphic SSR markers revealed three main groups of coconuts in Thailand. The identified SSR loci and SSR markers developed in this study will be useful for the study of coconut diversity and molecular breeding. The SSR mining approach used in this study could be applied to other plant species with a complex genome regardless of the availability of reference genome.

Download Full-text

Assessment of the Genetic Diversity of Rice Germplasms Characterized by Black-Purple and Red Pericarp Color Using Simple Sequence Repeat Markers

Plants ◽

10.3390/plants8110471 ◽

2019 ◽

Vol 8 (11) ◽

pp. 471

Author(s):

Jae-Ryoung Park ◽

Won-Tae Yang ◽

Yong-Sham Kwon ◽

Hyeon-Nam Kim ◽

Kyung-Min Kim ◽

...

Keyword(s):

Genetic Diversity ◽

Ssr Markers ◽

Simple Sequence Repeat ◽

Germplasm Collection ◽

Group Method ◽

Sequence Repeat ◽

Rice Varieties ◽

Red Pericarp ◽

Simple Sequence ◽

Colored Rice

The assessment of the genetic diversity within germplasm collections can be accomplished using simple sequence repeat (SSR) markers and association mapping techniques. The present study was conducted to evaluate the genetic diversity of a colored rice germplasm collection containing 376 black-purple rice samples and 172 red pericarp samples, conserved by Dong-A University. There were 600 pairs of SSR primers screened against 11 rice varieties. Sixteen informative primer pairs were selected, having high polymorphism information content (PIC) values, which were then used to assess the genetic diversity within the collection. A total of 409 polymorphic amplified fragments were obtained using the 16 SSR markers. The number of alleles per locus ranged from 11 to 47, with an average of 25.6. The average PIC value was 0.913, ranging from 0.855 to 0.964. Four hundred and nine SSR loci were used to calculate Jaccard’s distance coefficients, using the unweighted pair-group method with arithmetic mean cluster analysis. These accessions were separated into several distinctive groups corresponding to their morphology. The results provided valuable information for the colored rice breeding program and showed the importance of protecting germplasm resources and the molecular markers that can be derived from them.

Download Full-text

The new use of Sorghum bicolor-derived SSR markers to evaluate genetic diversity in 17 Australian Sorghum species

Plant Genetic Resources ◽

10.1079/pgr200454 ◽

2005 ◽

Vol 3 (1) ◽

pp. 19-28 ◽

Cited By ~ 12

Author(s):

Sally L. Dillon ◽

Peter K. Lawrence ◽

Robert J. Henry

Keyword(s):

Genetic Diversity ◽

Sorghum Bicolor ◽

Ssr Markers ◽

Diversity Indices ◽

Basic Knowledge ◽

Apparent Lack ◽

Breeding Programmes ◽

Diversity Studies ◽

Potential Use ◽

Simple Sequence

The Sorghum genus is extremely diverse both morphologically and geographically, however, relatively few of the 25 recognized species have been evaluated genetically. The apparent lack of basic knowledge pertaining to the levels of genetic diversity both within and between the 17 Australian wild species is a major obstacle to both their effective conservation and potential use in breeding programmes. Twelve Sorghum bicolor-derived simple sequence repeat (SSR) markers were evaluated for cross-species amplification in all 25 Sorghum species. The SSR markers were highly polymorphic, with diversity indices ranging from 0.59 to 0.99 with mean of 0.91. Five markers combined were able to differentiate 24 of the 25 Sorghum species, with intra-species polymorphism apparent. Sorghum bicolor-derived SSRs have proven to be an efficient source of markers for genetic diversity studies of the relatively poorly characterized Australian indigenous Sorghum species.

Download Full-text

ISSR Marker Based Genetic Diversity in Morinda Spp. For Its Enhanced Collection, Conservation and Utilization

10.21203/rs.3.rs-666059/v1 ◽

2021 ◽

Author(s):

Lalit Arya ◽

Ramya Kossery Narayanan ◽

Anjali Kak ◽

Chitra Devi Pandey ◽

Manjusha Verma ◽

...

Keyword(s):

Genetic Diversity ◽

Gene Diversity ◽

Inter Simple Sequence Repeat ◽

Issr Markers ◽

Morinda Citrifolia ◽

Species Differentiation ◽

Information Index ◽

Upgma Cluster Analysis ◽

Simple Sequence

Abstract Morinda (Rubiaceae) is considerably recognized for its multiple uses viz. food, medicine, dyes, firewood, tools, oil, bio-sorbent etc. The molecular characterization of such an important plant would be very useful for its multifarious enhanced utilization. In the present study, 31 Morinda genotypes belonging to two different species Morinda citrifolia and Morinda tomentosa collected from different regions of India were investigated using Inter Simple Sequence Repeat (ISSR) markers. Fifteen ISSR primers generated 176 bands with an average of 11.7 bands per primer, of which (90.34%) were polymorphic. The percentage of polymorphic bands, mean Nei’s gene diversity, mean Shannon’s information index in Morinda tomentosa and Morinda citrifolia was [(69.89%, 30.68%); (0.21 ± 0.19, 0.12 ± 0.20); (0.32 ± 0.27 0.17 ± 0.28)] respectively, revealing higher polymorphism and genetic diversity in Morinda tomentosa compared to Morinda citrifolia. Structure, and UPGMA cluster analysis placed the genotypes into well-defined separate clusters belonging to two species Morinda tomentosa and Morinda citrifolia revealing the utility of ISSR markers in species differentiation. Distinct ecotypes within a particular species could also be inferred emphasizing the collection and conservation of Morinda genotypes from different regions, in order to capture the overall diversity of respective species. Further higher diversity of M. tomentosa must be advanced for its utilization in nutraceutical, nutritional and other nonfood purposes.

Download Full-text