Application of wheat SSR markers for detection of genetic diversity in triticale (x Triticosecale witt. )

Present study aims to testify usefulness of particular wheat SSR markers for the detection of genetic diversity degree in the set of 59 triticale cultivars and new lines coming from different European countries and USA. For this purpose, a set of fifteen SSR markers were used. One SSR marker (Xwmc429) gave a uniform spectrum. The set of fourteen polymorphic markers provided 94 alleles with an average frequency of 6.71 alleles per locus. The number of alleles ranged between 2 (Xbarc 195) and 10 (Xbarc 137). Resulting from the number and frequency of alleles, diversity index (DI), polymorphic information content (PIC) and probabilities of identity (PI) were calculated. An average value of PIC for 14 markers was 0.640, the highest value was calculated for wheat SSR marker Xgwm 46 (0.809). Based on UPGMA algorithm, a dendrogram was constructed. It was able to separate 57 of 59 cultivars (96,6 %) from each other. American new-line NE-422T significantly separated from all cultivars and new lines. Only two french cultivars Bienvenu and Wilfried had not been separated from each other. A tested set of SSR markers allowed to better understand genetic relationships among European cultivars and American new lines. In general, a dendrogram along with results of calculated genetic indicators such as PIC, PI and DI point out at SSRs markers as high informative and usefull tool in genetic diversity research between close-related species.

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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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Molecular Diversity Analysis in Boro Rice (Oryza sativa L.) Landraces using SSR Markers

Asian Journal of Biology ◽

10.9734/ajob/2021/v12i130156 ◽

2021 ◽

pp. 36-48

Author(s):

Farhana Afrin Vabna ◽

Mohammad Zahidul Islam ◽

Md. Ferdous Rezwan Khan Prince ◽

Md. Ekramul Hoque

Keyword(s):

Genetic Diversity ◽

Ssr Markers ◽

Molecular Diversity ◽

Genetic Relationships ◽

Group Method ◽

Diversity Analysis ◽

Average Value ◽

Rice Landraces ◽

Boro Rice ◽

Research Institute

Aims: The aim of the study was to determine the genetic diversity of twenty four Boro rice landraces using rice genome specific twelve well known SSR markers. Study Design: Genomic DNA extraction, PCR amplification, Polyacrylamide gel electrophoresis (PAGE) and data analysis-these steps were followed to perform the research work. Data was analysed with the help of following software; POWERMAKER version 3.25, AlphaEaseFC (Alpha Innotech Corporation) version 4.0. UPGMA dendrogram was constructed using MEGA 5.1 software. Place and Duration of Study: The study was conducted at the Genetic Resources and Seed Division (GRSD), Bangladesh Rice Research Institute (BRRI), Joydebpur, Gazipur, Bangladesh during the period of November 2017 to March 2018. Methodology: Simple Sequence Repeat (SSR) markers were used to assay 24 landraces of Boro rice collected from the Gene Bank of Bangladesh Rice Research Institute (BRRI). Results: A total fifty four (54) alleles were detected, out of which forty five (45) polymorphic alleles were identified. The Polymorphic Information Content (PIC) of SSR markers ranged from 0.08 (RM447) to 0.84 (RM206) with an average value of PIC = 0.49. Gene diversity ranges from 0.08 (RM447) to 0.86 (RM206) with an average value of 0.52. The RM206 marker can be considered as the best marker among the studied markers for 24 rice landraces. Dendrogram based on Nei’s genetic distance using Unweighted Pair Group Method of Arithmetic Mean (UPGMA) indicated the segregation of 24 genotypes into three main clusters. Conclusion: The result revealed that SSR markers are very effective tools in the study of genetic diversity and genetic relationships and this result can be conveniently used for further molecular diversity analysis of rice genotypes to identify diverse parent for the development of high yielding variety in rice.

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Genetic diversity of mungbean (Vigna radiata L.) germplasm in Indonesia

Plant Genetic Resources ◽

10.1017/s1479262114000343 ◽

2014 ◽

Vol 12 (S1) ◽

pp. S91-S94 ◽

Cited By ~ 7

Author(s):

Puji Lestari ◽

Sue Kyung Kim ◽

Reflinur ◽

Yang Jae Kang ◽

Nurwita Dewi ◽

...

Keyword(s):

Genetic Diversity ◽

Ssr Markers ◽

Vigna Radiata ◽

Diversity Index ◽

Polymorphic Information Content ◽

Conservation Strategy ◽

Low Genetic Diversity ◽

Breeding Programmes ◽

The Mean ◽

Simple Sequence

Despite widespread mungbean [Vigna radiata (L.) Wilczek] consumption in Indonesia, few molecular studies have been carried out on accessions and available data are minimal. In this study, we used 30 newly developed simple sequence repeat (SSR) markers designed from the mapped sequence scaffolds of the Korean Sunhwanokdu and Gyeonggijaerae 5 mungbean genomes. These markers were used to examine loci in 83 mungbean accessions collected from diverse geographical areas in Indonesia. A total of 107 alleles were detected among the accessions with 29 polymorphic markers. However, the mean of polymorphic information content (0.33) value and diversity index (0.38) value was indicative of low genetic diversity in this germplasm. The mungbean population structure was not clearly differentiated and the number of subpopulations was unclear. Neighbour-joining tree analysis revealed that the genetic cluster did not reflect the geographical origin of the accessions. Interestingly, the most agriculturally improved varieties were genetically similar to some landraces from one of the main mungbean-producing regions. These newly developed SSR markers could be useful for detecting genetic variability as a basis for establishing a conservation strategy for mungbean germplasm with the aim of enhancing Indonesian breeding programmes.

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SSR allelic diversity in relation to morphological traits and resistance to grain mould in sorghum

Crop and Pasture Science ◽

10.1071/cp09192 ◽

2010 ◽

Vol 61 (3) ◽

pp. 230 ◽

Cited By ~ 4

Author(s):

Rajan Sharma ◽

S. P. Deshpande ◽

S. Senthilvel ◽

V. P. Rao ◽

V. Rajaram ◽

...

Keyword(s):

Genetic Diversity ◽

Ssr Markers ◽

Morphological Traits ◽

Ssr Marker ◽

Allelic Variation ◽

Gene Diversity ◽

Polymorphic Information Content ◽

Allelic Diversity ◽

Average Score ◽

Marker Loci

Allelic variation at 46 simple sequence repeat (SSR) marker loci well distributed across the sorghum genome was used to assess genetic diversity among 92 sorghum lines, 74 resistant and 18 susceptible to grain mould. Of the 46 SSR markers, 44 were polymorphic, with the number of alleles ranging from 2 to 20 with an average of 7.55 alleles per locus. Genetic diversity among the sorghum lines was high as indicated by polymorphic information content (PIC) and gene diversity values. PIC values of polymorphic SSR markers ranged from 0.16 to 0.90, with an average of 0.54. Gene diversity among the sorghum lines varied from 0.16 to 0.91, with an average score of 0.58 per SSR marker. AMOVA indicated that 12% of the total variation observed among the sorghum lines was accounted for between grain mould resistant and susceptible types. Diversity based on six morphological traits and grain mould scores indicated major roles of panicle type and glumes coverage, followed by grain colour, in clustering of the lines. Seven grain mould resistant/susceptible pairs with dissimilarity indices >0.50, but with similar flowering time, plant height, and panicle type/inflorescence within each pair, were selected for use in developing recombinant inbred line mapping populations to identify genomic regions (and quantitative trait loci) associated with sorghum grain mould resistance.

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Molecular marker diversity of SCN-resistant sources in soybean

Genome ◽

10.1139/g06-057 ◽

2006 ◽

Vol 49 (8) ◽

pp. 938-949 ◽

Cited By ~ 22

Author(s):

Yiwu Chen ◽

Dechun Wang ◽

Prakash Arelli ◽

Mohsen Ebrahimi ◽

Randall L Nelson

Keyword(s):

Genetic Diversity ◽

Ssr Markers ◽

Soybean Cyst Nematode ◽

Polymorphic Information Content ◽

Genetic Relationships ◽

Germplasm Collection ◽

Nematode Resistance ◽

The United States ◽

Cyst Nematode ◽

Clustering Methods

Soybean cyst nematode (SCN) (Heterodera glycines Ichinohe; HG) is one of the most destructive pests of soybean (Glycine max (L.) Merr.) in the United States. Over 100 SCN-resistant accessions within the USDA Soybean Germplasm Collection have been identified, but little is known about the genetic diversity of this SCN-resistant germplasm. The objective of this research was to evaluate the genetic variation and determine the genetic relationships among SCN-resistant accessions. One hundred twenty-two genotypes were evaluated by 85 simple sequence repeat (SSR) markers from 20 linkage groups. Non-hierarchical (VARCLUS) and hierarchical (Ward's) clustering were combined with multidimensional scaling (MDS) to determine relationships among tested lines. The 85 SSR markers produced 566 allelic fragments with a mean polymorphic information content (PIC) value of 0.35. The 122 lines were grouped into 7 clusters by 2 different clustering methods and the MDS results consistently corresponded to the assigned clusters. Assigned clusters were dominated by genotypes that possess one or more unique SCN resistance genes and were associated with geographical origins. The results of analysis of molecular variance (AMOVA) showed that the variation differences among clusters and individual lines were significant, but the differences among individuals within clusters were not significant.Key words: soybean cyst nematode resistance, genetic diversity, SSR markers, cluster analysis, soybean.

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Genetic Diversity of Seashore Paspalum Revealed with Simple Sequence Repeat Markers

Journal of the American Society for Horticultural Science ◽

10.21273/jashs04860-19 ◽

2020 ◽

Vol 145 (4) ◽

pp. 228-235

Author(s):

Qing Shen ◽

Hua Bian ◽

Hai-yan Wei ◽

Li Liao ◽

Zhi-yong Wang ◽

...

Keyword(s):

Genetic Diversity ◽

Simple Sequence Repeat ◽

Ssr Marker ◽

Diversity Index ◽

Polymorphic Information Content ◽

Principal Component ◽

Sequence Repeat ◽

Similarity Coefficients ◽

Seashore Paspalum ◽

Simple Sequence

Seashore paspalum (Paspalum vaginatum) is an important warm-season turfgrass distributed in tropical and coastal areas. It has excellent resistance to abiotic stresses, such as salinity, drought, and low temperature. However, the research on genetic diversity of local P. vaginatum collections from China is limited. In this study, the genetic diversity among 58 P. vaginatum accessions from four different provinces in China and four cultivars were assessed using simple sequence repeat (SSR) markers. The results indicated that a total of 45 alleles were detected by 19 polymorphic markers, with a range of 2 to 4 and an average of 2.4 alleles per marker. The genetic similarity coefficients between each pair of the 58 P. vaginatum accessions and four cultivars ranged from 0.51 to 1.00, with an average of 0.77. The range of variation of Shannon diversity index of each SSR marker was 0.047 to 1.075, with an average of 0.486. The polymorphic information content of each SSR marker varies from 0.016 to 0.577, with an average of 0.249. The results of cluster analysis and principal component analysis (PCA) showed that 58 P. vaginatum accessions and four cultivars were divided into four groups. These results provide the theoretical basis for the genetic diversity assessments and molecular marker–assisted breeding of P. vaginatum species.

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Assessment of Functional EST-SSR Markers (Sugarcane) in Cross-Species Transferability, Genetic Diversity among Poaceae Plants, and Bulk Segregation Analysis

Genetics Research International ◽

10.1155/2016/7052323 ◽

2016 ◽

Vol 2016 ◽

pp. 1-16 ◽

Cited By ~ 7

Author(s):

Shamshad Ul Haq ◽

Pradeep Kumar ◽

R. K. Singh ◽

Kumar Sambhav Verma ◽

Ritika Bhatt ◽

...

Keyword(s):

Genetic Diversity ◽

Segregation Analysis ◽

Polymorphic Information Content ◽

Genetic Relationships ◽

Average Density ◽

Grass Species ◽

Bulk Segregation Analysis ◽

After Effect ◽

Ssrs Markers ◽

Molecular Marker Development

Expressed sequence tags (ESTs) are important resource for gene discovery, gene expression and its regulation, molecular marker development, and comparative genomics. We procured 10000 ESTs and analyzed 267 EST-SSRs markers through computational approach. The average density was one SSR/10.45 kb or 6.4% frequency, wherein trinucleotide repeats (66.74%) were the most abundant followed by di- (26.10%), tetra- (4.67%), penta- (1.5%), and hexanucleotide (1.2%) repeats. Functional annotations were done and after-effect newly developed 63 EST-SSRs were used for cross transferability, genetic diversity, and bulk segregation analysis (BSA). Out of 63 EST-SSRs, 42 markers were identified owing to their expansion genetics across 20 different plants which amplified 519 alleles at 180 loci with an average of 2.88 alleles/locus and the polymorphic information content (PIC) ranged from 0.51 to 0.93 with an average of 0.83. The cross transferability ranged from 25% for wheat to 97.22% for Schlerostachya, with an average of 55.86%, and genetic relationships were established based on diversification among them. Moreover, 10 EST-SSRs were recognized as important markers between bulks of pooled DNA of sugarcane cultivars through BSA. This study highlights the employability of the markers in transferability, genetic diversity in grass species, and distinguished sugarcane bulks.

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Analyses of genetic diversity and population structure of anchote (Coccinia abyssinica (Lam.) Cogn.) using newly developed EST-SSR markers

Genetic Resources and Crop Evolution ◽

10.1007/s10722-021-01132-5 ◽

2021 ◽

Author(s):

Bekele Serbessa Tolera ◽

Kifle Dagne Woldegebriel ◽

Abel Teshome Gari ◽

Mulatu Geleta Dida ◽

Kassahun Tesfaye Geletu

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Ssr Markers ◽

Polymorphic Information Content ◽

Citrullus Lanatus ◽

Wide Range ◽

Minor Crop ◽

Ssrs Markers ◽

Expressed Sequence

AbstractAnchote (Coccinia abyssinica (Lam.) Cogn.) is a perennial root crop belonging to Cucurbitaceae family. It is endemic to Ethiopia and distributed over wide range of agro-ecologies. For further improvement and efficient conservation of this crop, characterization of its genetic diversity and its pattern of distribution is a vitally important step. Expressed sequence tags-simple sequence repeats (EST-SSRs) markers were developed from publicly available watermelon [Citrullus lanatus (Thunb.) Matsum. & Nakai] ESTs in the GenBank database. Among those novel markers, eight were polymorphic and subsequently used for genetic diversity and population structure analyses of 30 anchote accessions collected from western Ethiopia. A total of 24 alleles were obtained across the eight polymorphic loci and 30 accessions that revealed moderate level of genetic diversity in this minor crop. Among the eight loci, locus CA_06 was the most informative with six alleles and polymorphic information content (PIC) of 0.76. The accessions showed about threefold variation in terms of genetic diversity, with expected heterozygosity (He) ranging from 0.15 (accession An) to 0.44 (accession Dg). Other accessions with higher genetic diversity include Ar and Gu (He = 0.43 and 0.41, respectively). Analysis of molecular variance (AMOVA) revealed that the variation within accessions and among accessions accounted for 84.7% and 15.3% of the total variation, respectively. The study revealed low but significant population differentiation in this crop with no clear pattern of population structure. The EST-SSR markers developed in this study are the first of their kind for anchote and can be used for characterization of its wider genetic resources for conservation and breeding purposes.

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Genetic diversity among potato species as revealed by phenotypic resistances and SSR markers

Plant Genetic Resources ◽

10.1017/s1479262112000500 ◽

2013 ◽

Vol 11 (2) ◽

pp. 131-139 ◽

Cited By ~ 15

Author(s):

D. Carputo ◽

D. Alioto ◽

R. Aversano ◽

R. Garramone ◽

V. Miraglia ◽

...

Keyword(s):

Genetic Diversity ◽

Ssr Markers ◽

Sources Of Resistance ◽

Wild Potato Species ◽

Resistance Response ◽

Potato Species ◽

Average Value ◽

Ssr Analysis ◽

Efficient Breeding ◽

Resistant Genotypes

The evolutionary diversity of wild potato species makes them excellent materials for improving the narrow genetic basis of the cultivated potato Solanum tuberosum. Understanding their genetic diversity is important not only to choose the best parents for breeding, but also to design proper crossing schemes and selection strategies. The objectives of this study were to determine the resistance response to Ralstonia solanacearum, Potato virus Y and low temperatures of 21 clones of 12 potato species, and to determine their genetic diversity through simple sequence repeat (SSR) markers. Sources of resistance have been found for all the investigated traits, with high resistance variability not only between but also within species. Combined resistances were also identified, with positive implications for efficient breeding. SSR analysis allowed the detection of 12 loci and 46 alleles across all genotypes, with an average value of 3.8 alleles per locus. Both unique and rare alleles useful for marker-assisted selection were found. SSR-based cluster analysis revealed that resistant genotypes were distributed among all clusters, suggesting that genetically different resistant genotypes were identified. The information obtained in this study is discussed from a breeding perspective.

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Assessment of Genetic Diversity of Promising Castor Been (Ricinus communis L.) Genotypes in Nigeria

Notulae Scientia Biologicae ◽

10.15835/nsb11310346 ◽

2019 ◽

Vol 11 (3) ◽

pp. 467-474

Author(s):

Bolaji Zuluqurineen SALIHU ◽

Olamide Ahmed FALUSI ◽

Adeyinka Olufemi ADEPOJU ◽

Ibrahim Wasiu AROLU ◽

Oladipupo Yusuf DAUDU ◽

...

Keyword(s):

Genetic Diversity ◽

Diversity Index ◽

Gene Diversity ◽

Ricinus Communis ◽

Polymorphic Information Content ◽

Block Design ◽

Genetic Material ◽

Morphological Data ◽

Research Attention ◽

Ricinus Communis L

Castor oil plant (Ricinus communis L.) is an important oil crop with little research attention in Nigeria. In the present research, extent of genetic diversity among 20 Nigerian castor genotypes was determined using morphological descriptors and molecular markers. The genotypes were laid out on a randomized complete block design with three replicated plots. Molecular genotyping of the genotypes was carried out using genomic Simple Sequence Repeats (SSR). The genotypes revealed high divergence in seed colour, seed shape, seed mottle, seed caruncle and seed sizes. Seedling establishment varied from 70.18% (in Acc. 006) to 93.25% (Acc. 001) with average mean of 81.53%. Raceme length ranged from 15.90 cm to 29.54 cm with population mean of 20.80 cm. The highest seed yield (1222.98 kg/ha) was recorded in Acc. 001 and the least (611.46 kg/ha) was observed in Acc. 006. Seed oil content varied between 32.15% in Acc. 042 and 54.03% in Acc. 006. Agglomerative cluster dendrogram constructed from morphological data showed random distribution of the genotypes into three cluster groups irrespective of the sources/collection points. The genetic diversity based on SSR Marker Analysis revealed high average expected heterozygosity (0.74), Polymorphic information content (0.68), Nei’s gene diversity index (0.72) and Shannon's Information index (1.43). The dendrogram constructed from molecular data grouped the twenty genotypes into three groups at coefficient of 0.34. From these findings, it showed that the twenty genotypes evaluated are divergent in nature and they could serve as good genetic material for castor breeding in Nigeria.

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