scholarly journals Intra- Cultivar Variability Endorsed by SSR Markers in Mango

2018 ◽  
Vol 15 (1) ◽  
pp. 181-186
Author(s):  
Anju Bajpai ◽  
Nimisha Sharma ◽  
Navin Srivastava ◽  
Shailendra Rajan ◽  
Muthukumar. M
Keyword(s):  
Ssr Markers ◽  
Gene Diversity ◽  
Polymorphic Information Content ◽  
Morphological Variability ◽  
Minimum Variance ◽  
Statistical Parameters ◽  
Genomic Variations ◽  
Land Race ◽  
Marker Loci ◽  
Cultivar Variation

Appreciable intra cultivar variation has warranted clonal selections, which has emerged as an important tool in mango breeding. This important source of morphological variability manifested in altered fruit and quality attributes has yielded improved clones in India and abroad, few of which were exposed to SSR based analysis. Statistical parameters viz., Polymorphic Information Content (0.319 in MiIIHR12 to 0.819 for MiIIHR26) and Gene Diversity (0.399 in MiIIHR12 to 0.839 for MiIIHR26), defined the ability of the chosen SSR markers to discriminate the intra cultivar variability, besides highlighting the extent of diversity captured by the improved clones. Furthermore, genetic relationship among the clones derived by Wards minimum variance, placed Himsagar and Langra clones in Cluster I and II respectively, Himsagar recording high genetic heterogeneity within its cluster, intra cultivar variability being 0.16-0.916, thus showing suitability for breeding by clonal selections. Even the use of limited SSR marker loci (6), could reveal and document the genomic variations accounting for the variations in the Dashehari clones as well as placing land race ‘Suraiyya’, as an out-group. The sampled clones of elite variety Chausa did not show any variation at the studied marker loci, thus exposing limited heterogeneity in the clones and demanding more explorations for breeding superior types targeting regularity in bearing.

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

2010 ◽  
Vol 61 (3) ◽  
pp. 230 ◽  
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.

AFLP and SSR analysis of genetic diversity among landraces of bread wheat (Triticum aestivum L. em. Thell) from different geographic regions

2005 ◽  
Vol 56 (7) ◽  
pp. 691 ◽  
Author(s):  
B. J. Stodart ◽  
M. Mackay ◽  
H. Raman
Keyword(s):  
Genetic Diversity ◽  
Middle East ◽  
Bread Wheat ◽  
Ssr Markers ◽  
North Africa ◽  
Gene Diversity ◽  
Polymorphic Information Content ◽  
Triticum Aestivum L ◽  
Southern Europe ◽  
Germplasm Collections

A set of 44 bread wheat landraces was used to determine the efficacy of 16 amplifed fragment length polymorphism (AFLP) primers and 63 wheat simple sequence repeat (SSR) markers in identifying polymorphisms between accessions. The SSR markers detected approximately 10 alleles per locus with a mean gene diversity (Hz) of 0.63, whereas AFLP primers identified approximately 147 fragments per primer with a mean gene diversity of 0.25. A set of 54 SSR markers and 11 AFLP primers was identified as highly polymorphic (polymorphic information content (PIC) ≥ 0.5 and 0.3 for SSR and AFLP, respectively), and suitable for molecular characterisation of germplasm. Principle coordinate analysis suggested that the AFLP and SSR loci could be used to discriminate among accessions collected from North Africa and southern Europe from those collected from the Middle East. Both marker types indicate that accessions from North Africa and southern Europe, the Middle East, and southern and eastern Asia are genetically diverse. The results indicate the usefulness of the molecular markers to assess genetic diversity present within germplasm collections.

scholarly journals Genetic diversity among tropical maize inbred lines as revealed by SSR markers

2020 ◽  
pp. 2010-2019
Author(s):  
Maizura Abu Sin ◽  
Ghizan Saleh ◽  
Nur Ashikin Psyquay Abdullah ◽  
Pedram Kashiani
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Gene Diversity ◽  
Polymorphic Information Content ◽  
Similarity Index ◽  
Inbred Lines ◽  
Hybrid Breeding ◽  
Heterotic Groups ◽  
Breeding Programs ◽  
Maize Inbred Lines

Genetic diversity and phenotypic superiority are important attributes of parental inbred lines for use in hybrid breeding programs. In this study, genetic diversity among 30 maize (Zea mays L.) inbred lines comprising of 28 introductions from the International Maize and Wheat Improvement Center (CIMMYT), one from Indonesia and a locally developed, were evaluated using 100 simple sequence repeat (SSR) markers, as early screening for potential parents of hybrid varieties. All markers were polymorphic, with a total of 550 unique alleles detected on the 100 loci from the 30 inbred lines. Allelic richness ranged from 2 to 13 per locus, with an average of 5.50 alleles (na). Number of effective alleles (ne) was 3.75 per locus, indicating their high effectiveness in revealing diversity among inbred lines. Average polymorphic information content (PIC) was 0.624, with values ranging from 0.178 to 0.874, indicating high informativeness of the markers. High gene diversity was observed on Chromosomes 8 and 4, with high number of effective alleles, indicating their potential usefulness for QTL analysis. The UPGMA dendrogram constructed identified four heterotic groups within a similarity index of 0.350, indicating that these markers were able to group the inbred lines. The three-dimensional PCoA plot also supports the dendrogram grouping, indicating that these two methods complement each other. Inbred lines in different heterotic groups have originated from different backgrounds and population sources. Information on genetic diversity among the maize inbred lines are useful in developing strategies exploiting heterosis in breeding programs

Genetic structure of wild emmer wheat populations as reflected by transcribed versus anonymous SSR markers

Genome ◽  
2008 ◽  
Vol 51 (3) ◽  
pp. 187-195 ◽  
Author(s):  
Zvi Peleg ◽  
Tzion Fahima ◽  
Shahal Abbo ◽  
Tamar Krugman ◽  
Yehoshua Saranga
Keyword(s):  
Genetic Structure ◽  
Ssr Markers ◽  
Expressed Sequence Tag ◽  
Triticum Turgidum ◽  
Gene Diversity ◽  
Polymorphic Information Content ◽  
Allelic Diversity ◽  
Wild Emmer Wheat ◽  
Emmer Wheat ◽  
Wild Emmer

Simple sequence repeat (SSR) markers have become a major tool in population genetic analyses. The anonymous genomic SSRs (gSSRs) have been recently supplemented with expressed sequence tag (EST) derived SSRs (eSSRs), which represent the transcribed regions of the genome. In the present study, we used 8 populations of wild emmer wheat ( Triticum turgidum subsp. dicoccoides ) to compare the usefulness of the two types of SSR markers in assessing allelic diversity and population structure. gSSRs revealed significantly higher diversity than eSSRs in terms of average number of alleles (14.92 vs. 7.4, respectively), polymorphic information content (0.87 vs. 0.68, respectively), and gene diversity (He; 0.55 vs. 0.38, respectively). Despite the overall differences in the level of diversity, Mantel tests for correlations between eSSR and gSSR pairwise genetic distances were found to be significant for each population as well as for all accessions jointly (RM = 0.54, p = 0.01). Various genetic structure analyses (AMOVA, PCoA, STRUCTURE, unrooted UPGMA tree) revealed a better capacity of eSSRs to distinguish between populations, while gSSRs showed a higher proportion of intrapopulation (among accessions) diversity. We conclude that eSSR and gSSR markers should be employed in conjunction to obtain a high inter- and intra-specific (or inter- and intra-varietal) distinctness.

scholarly journals Construction of a Core Collection of Native Perilla Germplasm Collected From South Korea Based on SSR Markers and Morphological Characteristics

2021 ◽  
Author(s):  
Kyu Jin Sa ◽  
Dong Min Kim ◽  
Jun Seok Oh ◽  
Hyeon Park ◽  
Do Yoon Hyun ◽  
...  
Keyword(s):  
South Korea ◽  
Ssr Markers ◽  
Core Collection ◽  
Morphological Traits ◽  
Gene Diversity ◽  
Polymorphic Information Content ◽  
Morphological Characteristics ◽  
Diversity Indices ◽  
The Core ◽  
Long Time

Abstract The leaves and seed oil of Perilla crop (Perilla frutescens L.) have attracted interest as health foods in East Asia. This crop has been traditionally cultivated and used for a long time as a folk plant, especially in Korea. In our study, the 22 SSR markers and six morphological traits were used to assess the genetic diversity and population structure, to select a core collection of 400 Perilla accessions conserved in the RDA-Genebank of South Korea. A total of 173 alleles were detected and the number of alleles per locus ranged from 4 to 15 (average = 7.9). Gene diversity and polymorphic information content ranged from 0.138 to 0.868 (average = 0.567) and 0.134 to 0.853 (average = 0.522), respectively. The 400 accessions were not clearly distinguished geographically by STRUCTURE and UPGMA analyses. A core collection (44 accessions) was selected from the entire collection by using PowerCore. The core collection accounted for 11.0% of the entire Perilla collection, including 100% of the number of alleles maintained in the whole collection and with similar or greater Shannon-Weaver and Nei diversity indices than the whole collection. The core collection selected by SSR markers was evenly distributed in three clusters on a scatter plot by six morphological traits. The first core collection of Perilla accessions was constructed, and it maintained allelic richness. Further modification of the core collection is expected with the continuous addition of new accessions of the two cultivated types of Perilla crop and their weedy types.

scholarly journals Molecular characterization of barley (Hordeum vulgare L.) accessions of the Serbian GeneBank by SSR fingerprinting

Genetika ◽  
2013 ◽  
Vol 45 (1) ◽  
pp. 167-180 ◽  
Author(s):  
Gordana Surlan-Momirovic ◽  
Ilona Krämer ◽  
Kamenko Bratkovic ◽  
Miroslav Zoric ◽  
Una Momirovic ◽  
...  
Keyword(s):  
Hordeum Vulgare ◽  
Ssr Markers ◽  
Clustering Algorithm ◽  
Growth Habit ◽  
Gene Diversity ◽  
Polymorphic Information Content ◽  
Mean Value ◽  
Group Method ◽  
Hordeum Vulgare L ◽  
Shared Allele

Molecular diversity of 145 barley (Hordeum vulgare subsp. vulgare L.) accessions from the Serbian GenBank was assessed by single sequence repeats (SSR) markers. A set of 15 SSRs, covering all chromosomes of the diploid barley genome with 2-3 SSR markers per chromosome, with a range of 4-18 alleles per locus were used. In total, 15 loci and 119 alleles were detected, with an average of 7.93 alleles per locus. The Polymorphic information content value ranged from 0.220 to 0.782 with a mean value of 0.534. Regarding the growth habit and row type groups, gene diversity was comparatively higher for the spring (0.616) and six-rowed accessions (0.616) than for the winter and two- rowed accessions (0.322 and 0.478, respectively). Analysis of molecular variance showed that all sources of variation were significant (P < 0.01), but the between-group component was predominant (76.85%) for growth habit and 89.45% for row type. Unweighted Pair Group Method with Arithmetic Mean (UPGMA) cluster analysis based on the shared allele distance (DSA) matrix estimated on the SSR data assigned the genotypes into two clusters - the first smaller consisting of the six 6-rowed spring cultivars and the second comprising six subclusters. Genotype MBR1012 was separated from all other genotypes that constitute UPGMA tree. The associations of genotypes belonging to different growth habit and row type groups were assessed using Principal Coordinate Analysis revealing separation of winter growth habit group from facultative one. The use of the STRUCTURE clustering algorithm allowed the identification of 2 subpopulations of genotypes.

Haplotype analysis of Saltol QTL region in diverse landraces, wild rice and introgression lines of rice (Oryza sativa L.)

2021 ◽  
pp. 1-10
Author(s):  
K. K. Manohara ◽  
Shaiesh Morajkar ◽  
Yogini Shanbhag ◽  
Pratham Phadte ◽  
Nagendra Kumar Singh
Keyword(s):  
Salt Stress ◽  
Ssr Markers ◽  
Salinity Tolerance ◽  
Wild Rice ◽  
Haplotype Analysis ◽  
Oryza Sativa L ◽  
Gene Diversity ◽  
Polymorphic Information Content ◽  
Seedling Stage ◽  
Chromosome 1

Abstract Salt stress is a major abiotic stress affecting the productivity of rice crop worldwide. This study screened a set of 71 rice genotypes collected from coastal parts of Goa and Karnataka states in India for seedling stage salinity tolerance to identify genotypes alternative to standard salt-tolerant donors Pokkali, FL478, etc. Phenotyping for seedling stage tolerance was carried out under micro plots at an induced salinity of 12 dS/m. For haplotyping, 14 Saltol QTL linked simple sequence repeat (SSR) markers on chromosome 1 were utilized. On the basis of the response to salt stress, 10 genotypes were found tolerant, 16 moderately tolerant, 29 sensitive and 15 as highly sensitive. Among the SSR markers, marker RM10871 was the most polymorphic with a polymorphic information content of 0.90, exhibiting 14 different alleles followed by RM10793 (0.84) and RM3412 (0.80) with 8 and 7 alleles, respectively. These markers also exhibited high values for the effective number of alleles (Ne) and gene diversity (I). The haplotype analysis revealed that the allelic constitution of the Saltol region of 10 tolerant genotypes from our study varied in comparison to the reference tolerant check FL478. Further, the haplotype of three tolerant genotypes, namely, Goa Dhan 2, Panvel 1 and Goa wild rice (GWR) 005 appears to be completely different from the FL478 haplotype indicating tolerance in these genotypes is controlled by genomic region other than Saltol. These three genotypes with probable novel regions for seedling stage salt tolerance can be considered for enhancing salinity tolerance of rice cultivars.

scholarly journals Genetic Diversity of Torch Ginger (Etlingera elatior) Germplasm Revealed by ISSR and SSR Markers

2019 ◽  
Vol 2019 ◽  
pp. 1-14 ◽  
Author(s):  
Nor Asiah Ismail ◽  
M. Y. Rafii ◽  
T. M. M. Mahmud ◽  
M. M. Hanafi ◽  
Gous Miah
Keyword(s):  
Genetic Diversity ◽  
Molecular Markers ◽  
Ssr Markers ◽  
Gene Diversity ◽  
Polymorphic Information Content ◽  
Allelic Diversity ◽  
Germplasm Collection ◽  
Peninsular Malaysia ◽  
Molecular Characteristics ◽  
Etlingera Elatior

Fifty-seven accessions of torch ginger (Etlingera elatior) collected from seven states in Peninsular Malaysia were evaluated for their molecular characteristics using ISSR and SSR markers to assess the pattern of genetic diversity and association among the characteristics. Diversity study through molecular characterization showed that high variability existed among the 57 torch ginger accessions. ISSR and SSR molecular markers revealed the presence of high genetic variability among the torch ginger accessions. The combination of different molecular markers offered reliable and convincing information about the genetic diversity of torch ginger germplasm. This study found that SSR marker was more informative compared to ISSR marker in determination of gene diversity, polymorphic information content (PIC), and heterozygosity in this population. SSR also revealed high ability in evaluating diversity levels, genetic structure, and relationships of torch ginger due to their codominance and rich allelic diversity. High level of genetic diversity discovered by SSR markers showed the effectiveness of this marker to detect the polymorphism in this germplasm collection.

scholarly journals Genetic Analysis for Mapping of Physiological Traits Related to Seed Vigour in Rice Through Association Mapping

2021 ◽  
Author(s):  
Priyadarshini Sanghamitra ◽  
Deepak Kumar nayak ◽  
saumya ranjan Barik ◽  
Elssa Pandit ◽  
Ramakrushna Bastia ◽  
...  
Keyword(s):  
Growth Rate ◽  
Linear Model ◽  
Ssr Markers ◽  
Gene Diversity ◽  
Polymorphic Information Content ◽  
Germination Rate ◽  
Physiological Traits ◽  
Seed Vigour ◽  
Vigour Index ◽  
Good Quality Seed

Abstract Background:Good quality seed is an important factor for a good crop. Vigor is the key performing trait of quality seed. Genomic regions controlling the physiological traits related to seed vigour are not fully reported.Results: A panel was prepared by including genotypes from all the groups of the fifteen physiological traits representing a population of 250 germplasm lines. Wide variations were observed for the 15 physiological traits in the population. The population was classified into 6 genetic groups. Presence of linkage disequilibrium (LD) was detected in the panel population based on the fixation indices of the subpopulations. Moderate values of gene diversity, polymorphic information content (PIC) and other diversity parameters were estimated from the population by genotyping with 109 SSR markers. The population was classified into subpopulations and sub-clusters showed relation with the genotypes for their physiological traits. Ten physiological traits were detected to be significantly associated with SSR markers analyzed by both the General linear model (GLM) and Mixed linear model (MLM). A total of 19 novel QTLs controlling different physiological traits namely qGP 6.2 and qGP 8.2 for germination % (GP); qGR 9.1 for germination rate (GR); qGI 1.2, qGI 6.1, qGI 8.1, qGI 11.1 and qGI 12.1 for germination index (GI); qRPE1.1 and qRPE8.1 for rate of plumule elongation (RPE); qAGR 8.1 for AGR; qRSG1.2 and qRSG12.2 for rate of shoot growth (RSG); qRGR3.1 and qRGR11.1 for relative growth rate (RGR); qSVI 1.1 for seed vigour index I (SVI I); qSVII 1.1, qSVII3.1, and qSVII12.1 for seed vigour index II (SVI II), and qRRG8.1 for relative root growth rate were identified. The reported QTL for root length, qRL11.1 was validated in this mapping population. Additionally, QTLs, qRPE8.1 and qAGR8.1 of traits, RPE and AGR; qGI 6.1 and qGP6.2 of GI and GP; qGI 11.1 and qRL11.1 of GI and RL; qAGR8.1 and qRRG8.1 of AGR and RRG, and qRSG3.1 and qRGR3.1of traits RSG and RGR were detected for co-localization or co-inheritance. Conclusion: The traits identified and markers detected in the association analysis will be useful for improvement of seed vigour trait through marker-assisted selection in rice.

scholarly journals Microsatellite Based Diversity Analysis and the Development of Core-Set Germplasm in Pakistani Barley Lines

2019 ◽  
Author(s):  
Murad Ali ◽  
Ping Yang ◽  
Manzoor Hussain ◽  
Mohammad Nisar ◽  
Niaz Ali ◽  
...  
Keyword(s):  
Population Structure ◽  
Ssr Markers ◽  
Ssr Marker ◽  
Gene Diversity ◽  
Polymorphic Information Content ◽  
Mean Value ◽  
Germplasm Resources ◽  
Barley Cultivars ◽  
Core Set ◽  
Population Structure Analysis

Abstract Background Illustrating the population structure and genetic diversity in selected germplasm resources (after three year multi locations trials) plays a key role which directly utilize the selection of lines in a population for accumulative trait breeding in crops.Results In order to further understand, the structure of population and genetic variability, we explored a core set of 100 lines (selected from 600 genotypes) in multi-location trials for three years (2016-2019) in Dir Lower, Swat, Khyber Pukhtonkhwa Pakistan and China with 33 SSR markers. The integrated population structure analysis in a core of hundred germplasm with Pakistani origin with three approved commercial barley cultivars have strong stratification that allowed their division into four major subpopulations (i.e. PI, PII, PIII and PIV) and an admixture subpopulation, with 52, 9, 15 and 27 germplasm respectively. A total of 133 alleles were identified with mean value of 0.80 Polymorphic information content. The number of alleles detected by the system varied from two alleles amplified to as six with an average of 4.03 per SSR marker pair. The gene diversity ranged from 0.56 to 0.98 with an average of 0.82 in selected germplasm resources. Based on the SSR data, the 100 selected germplasm with three cultivars were classified into four main phylogenetic Linages (LI, LII, LIII and LIV) which corresponded to the phylogenic grouping in genotypes.Conclusion We assembled a core set of 20 barley genotypes (~1/5 of original population size) to sustain sufficient mapping of SSR marker with Phenotype, in which we proposed four SSR markers, Bmac0040, Bmac0134, Bmag0125 and Bmag0211 for malt gene and marker (Bmac0399) for tolerance to salinity gene, which will be applicable for marker assisted breeding in barley gene resources.

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